October 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2809: Allow for a specified target for display links...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3bd7acfe34cc changeset: 2809:3bd7acfe34cc user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Sep 30 15:35:05 2009 -0400 description: Allow for a specified target for display links, rahter than forcing it to be _blank - this will allow external tools like GeneTrack to run inside the Galaxy frame set. 3 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/tracks.py templates/root/history_common.mako diffs (64 lines): diff -r 9cc7a17e0ac7 -r 3bd7acfe34cc lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Wed Sep 30 14:47:17 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Wed Sep 30 15:35:05 2009 -0400 @@ -171,11 +171,11 @@ def get_mime(self): """Returns the mime type of the datatype""" return 'application/octet-stream' - def add_display_app (self, app_id, label, file_function, links_function ): + def add_display_app ( self, app_id, label, file_function, links_function ): """ Adds a display app to the datatype. app_id is a unique id - label is the primary display label, ie display at 'UCSC' + label is the primary display label, e.g., display at 'UCSC' file_function is a string containing the name of the function that returns a properly formatted display links_function is a string containing the name of the function that returns a list of (link_name,link) """ @@ -205,7 +205,7 @@ except: log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible' % (self.supported_display_apps[type]['file_function'], self.__class__.__name__, type) ) return "This display type (%s) is not implemented for this datatype (%s)." % ( type, dataset.ext) - def get_display_links(self, dataset, type, app, base_url, **kwd): + def get_display_links( self, dataset, type, app, base_url, target_frame='_blank', **kwd ): """ Returns a list of tuples of (name, link) for a particular display type. No check on 'access' permissions is done here - if you can view the dataset, you can also save it @@ -214,7 +214,7 @@ """ try: if type in self.get_display_types(): - return getattr (self, self.supported_display_apps[type]['links_function']) (dataset, type, app, base_url, **kwd) + return target_frame, getattr ( self, self.supported_display_apps[type]['links_function'] ) ( dataset, type, app, base_url, **kwd ) except: log.exception( 'Function %s is referred to in datatype %s for generating links for type %s, but is not accessible' \ % ( self.supported_display_apps[type]['links_function'], self.__class__.__name__, type ) ) diff -r 9cc7a17e0ac7 -r 3bd7acfe34cc lib/galaxy/datatypes/tracks.py --- a/lib/galaxy/datatypes/tracks.py Wed Sep 30 14:47:17 2009 -0400 +++ b/lib/galaxy/datatypes/tracks.py Wed Sep 30 15:35:05 2009 -0400 @@ -27,6 +27,8 @@ def __init__(self, **kwargs): super( GeneTrack, self ).__init__( **kwargs ) self.add_display_app( 'genetrack', 'View in GeneTrack', '', 'genetrack_link' ) + def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ): + return data.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd ) def genetrack_link( self, hda, type, app, base_url ): ret_val = [] if hda.has_data: diff -r 9cc7a17e0ac7 -r 3bd7acfe34cc templates/root/history_common.mako --- a/templates/root/history_common.mako Wed Sep 30 14:47:17 2009 -0400 +++ b/templates/root/history_common.mako Wed Sep 30 15:35:05 2009 -0400 @@ -83,11 +83,11 @@ <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> | <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main">rerun</a> %for display_app in data.datatype.get_display_types(): - <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> + <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> %if len( display_links ) > 0: | ${data.datatype.get_display_label(display_app)} %for display_name, display_link in display_links: - <a target="_blank" href="${display_link}">${_(display_name)}</a> + <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> %endfor %endif %endfor

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[hg] galaxy 2806: Fix reporting number of regions processed in M...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/268ab95fc8a7 changeset: 2806:268ab95fc8a7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Sep 30 14:06:06 2009 -0400 description: Fix reporting number of regions processed in MAF Stats tool. 1 file(s) affected in this change: tools/maf/maf_stats.py diffs (22 lines): diff -r c63a444cd7ba -r 268ab95fc8a7 tools/maf/maf_stats.py --- a/tools/maf/maf_stats.py Wed Sep 30 11:40:09 2009 -0400 +++ b/tools/maf/maf_stats.py Wed Sep 30 14:06:06 2009 -0400 @@ -54,7 +54,7 @@ out = open(output_filename, 'w') - num_region = 0 + num_region = None species_summary = {} total_length = 0 #loop through interval file @@ -97,7 +97,8 @@ for spec in species_summary: out.write( "%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float( species_summary[spec] ) / total_length ) ) out.close() - print "%i regions were processed with a total length of %i." % ( num_region, total_length ) + if num_region is not None: + print "%i regions were processed with a total length of %i." % ( num_region + 1, total_length ) maf_utilities.remove_temp_index_file( index_filename ) if __name__ == "__main__": __main__()

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[hg] galaxy 2807: Added text trimmer that can be used to groom f...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/aafecc059ba6 changeset: 2807:aafecc059ba6 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Wed Sep 30 14:11:01 2009 -0400 description: Added text trimmer that can be used to groom fastq data 6 file(s) affected in this change: test-data/trimmer_a_f_c0_s1_e13_i62.dat test-data/trimmer_a_f_c2_s1_e2_i62.dat test-data/trimmer_tab_delimited.dat tool_conf.xml.sample tools/filters/trimmer.py tools/filters/trimmer.xml diffs (273 lines): diff -r 268ab95fc8a7 -r aafecc059ba6 test-data/trimmer_a_f_c0_s1_e13_i62.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmer_a_f_c0_s1_e13_i62.dat Wed Sep 30 14:11:01 2009 -0400 @@ -0,0 +1,5 @@ +12345 abcdef +67890 ghjkl g +>assa lljlj ljlj +sasas hghg hg +@dgf gfgf gfg diff -r 268ab95fc8a7 -r aafecc059ba6 test-data/trimmer_a_f_c2_s1_e2_i62.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmer_a_f_c2_s1_e2_i62.dat Wed Sep 30 14:11:01 2009 -0400 @@ -0,0 +1,5 @@ +12345 ab xyz +67890 gh ghjt +>assa lljlj ljlj +sasas hg hghg +@dgf gf gfgf diff -r 268ab95fc8a7 -r aafecc059ba6 test-data/trimmer_tab_delimited.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmer_tab_delimited.dat Wed Sep 30 14:11:01 2009 -0400 @@ -0,0 +1,5 @@ +12345 abcdef xyz +67890 ghjkl ghjt +>assa lljlj ljlj +sasas hghg hghg +@dgf gfgf gfgf diff -r 268ab95fc8a7 -r aafecc059ba6 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed Sep 30 14:06:06 2009 -0400 +++ b/tool_conf.xml.sample Wed Sep 30 14:11:01 2009 -0400 @@ -45,6 +45,7 @@ <tool file="filters/remove_beginning.xml" /> <tool file="filters/headWrapper.xml" /> <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /> </section> <section name="Filter and Sort" id="filter"> <tool file="stats/filtering.xml" /> diff -r 268ab95fc8a7 -r aafecc059ba6 tools/filters/trimmer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/trimmer.py Wed Sep 30 14:11:01 2009 -0400 @@ -0,0 +1,108 @@ +#!/usr/bin/env python + +import sys +import optparse + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def main(): + usage = """%prog [options] + +options (listed below) default to 'None' if omitted + """ + parser = optparse.OptionParser(usage=usage) + + parser.add_option( + '-a','--ascii', + dest='ascii', + action='store_true', + default = False, + help='Use ascii codes to defined ignored beginnings instead of raw characters') + + parser.add_option( + '-q','--fastq', + dest='fastq', + action='store_true', + default = False, + help='The input data in fastq format. It selected the script skips every even line since they contain sequence ids') + + parser.add_option( + '-i','--ignore', + dest='ignore', + help='A comma separated list on ignored beginnings (e.g., ">,@"), or its ascii codes (e.g., "60,42") if option -a is enabled') + + parser.add_option( + '-s','--start', + dest='start', + default = '0', + help='Trim from beginning to here (1-based)') + + parser.add_option( + '-e','--end', + dest='end', + default = '0', + help='Trim from here to the ned (1-based)') + + parser.add_option( + '-f','--file', + dest='input_txt', + default = False, + help='Name of file to be chopped. STDIN is default') + + parser.add_option( + '-c','--column', + dest='col', + default = '0', + help='Column to chop. If 0 = chop the whole line') + + + options, args = parser.parse_args() + invalid_starts = [] + + if options.input_txt: + infile = open ( options.input_txt, 'r') + else: + infile = sys.stdin + + if options.ignore and options.ignore != "None": + invalid_starts = options.ignore.split(',') + + if options.ascii and options.ignore and options.ignore != "None": + for i, item in enumerate( invalid_starts ): + invalid_starts[i] = chr( int( item ) ) + + col = int( options.col ) + + for i, line in enumerate( infile ): + line = line.rstrip( '\r\n' ) + if line: + + if options.fastq and i % 2 == 0: + print line + continue + + if options.fastq and line.startswith('@'): + stop_err('Malformed fastq file: even numbered line starts with @') + + if line[0] not in invalid_starts: + if col == 0: + if int( options.end ) > 0: + line = line[ int( options.start )-1 : int( options.end ) ] + else: + line = line[ int( options.start )-1 : ] + else: + fields = line.split( '\t' ) + if col-1 > len( fields ): + stop_err('Column %d does not exist. Check input parameters\n' % col) + + if int( options.end ) > 0: + fields[col - 1] = fields[col - 1][ int( options.start )-1 : int( options.end ) ] + else: + fields[col - 1] = fields[col - 1][ int( options.start )-1 : ] + line = '\t'.join(fields) + print line + +if __name__ == "__main__": main() + diff -r 268ab95fc8a7 -r aafecc059ba6 tools/filters/trimmer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/trimmer.xml Wed Sep 30 14:11:01 2009 -0400 @@ -0,0 +1,119 @@ +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description> + <command interpreter="python"> + chopper.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs> + <param format="tabular,text" name="input1" type="data" label="this dataset"/> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> + <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/> + <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> + <option value="-q">Yes</option> + <option value="">No</option> + </param> + <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed"> + <option value="62">></option> + <option value="64">@</option> + <option value="43">+</option> + <option value="60"><</option> + <option value="42">*</option> + <option value="45">-</option> + <option value="61">=</option> + <option value="124">|</option> + <option value="63">?</option> + <option value="36">$</option> + <option value="46">.</option> + <option value="58">:</option> + <option value="38">&</option> + <option value="37">%</option> + <option value="94">^</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="trimmer_tab_delimited.dat"/> + <param name="col" value="0"/> + <param name="start" value="1"/> + <param name="end" value="13"/> + <param name="ignore" value="62"/> + <param name="fastq" value="No"/> + <output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/> + </test> + <test> + <param name="input1" value="trimmer_tab_delimited.dat"/> + <param name="col" value="2"/> + <param name="start" value="1"/> + <param name="end" value="2"/> + <param name="ignore" value="62"/> + <param name="fastq" value="No"/> + <output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/> + </test> + + </tests> + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: + + 1234567890 + abcdefghijk + +by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: + + 23456 + bcdef + +----- + +**Eaxmple 2** + +Trimming column 2 of this dataset:: + + bcde 12345 fghij 67890 + fghij 67890 abcde 12345 + +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: + + abcde 234 fghij 67890 + fghij 789 abcde 12345 + +----- + +**Trimming FASTQ datasets** + +This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected *Yes* from the **Is input dataset in fastq format?** dropdown. If set to *Yes*, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset:: + + @081017-and-081020:1:1:1715:1759 + GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC + + + II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B + +cab done by setting **Remove everything from this position to the end** to 31:: + + @081017-and-081020:1:1:1715:1759 + GGACTCAGATAGTAATCCACGCTCCTTTAAA + + + II#IIIIIII$5+.(9IIIIIII$%*$G$A3 + +**Note** that headers are skipped. + +.. class:: warningmark + +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool>

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[hg] galaxy 2805: Requests functional tests: fixed a hack in use...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c63a444cd7ba changeset: 2805:c63a444cd7ba user: rc date: Wed Sep 30 11:40:09 2009 -0400 description: Requests functional tests: fixed a hack in user address creation 1 file(s) affected in this change: test/functional/test_forms_and_requests.py diffs (60 lines): diff -r 3e5428b298b1 -r c63a444cd7ba test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Wed Sep 30 10:40:08 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Wed Sep 30 11:40:09 2009 -0400 @@ -12,14 +12,14 @@ ( 'Received', 'Sample tube received' ), ( 'Done', 'Sequence run complete' ) ] address1 = dict( short_desc="Office", - name="James Bond", + name="James+Bond", institution="MI6" , - address1="MI6 Headquaters", + address1="MI6+Headquarters", address2="", city="London", state="London", postal_code="007", - country="United Kingdom", + country="United+Kingdom", phone="007-007-0007" ) @@ -165,26 +165,21 @@ self.visit_url( '%s/library_admin/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) # create address - #self.create_address( user_address1 ) - #self.check_page_for_string( 'Address <b>%s</b> has been added' % user_address1[ 'short_desc' ] ) - ## TODO: FIX HACK - ## the user address creation should be done as a test. + self.logout() + self.login( email='test1(a)bx.psu.edu' ) + self.home() + url_str = '%s/user/new_address?short_desc=%s&name=%s&institution=%s&address1=%s&address2=%s&city=%s&state=%s&postal_code=%s&country=%s&phone=%s' \ + % ( self.url, address1[ 'short_desc' ], address1[ 'name' ], address1[ 'institution' ], + address1[ 'address1' ], address1[ 'address2' ], address1[ 'city' ], address1[ 'state' ], + address1[ 'postal_code' ], address1[ 'country' ], address1[ 'phone' ] ) + print url_str + self.visit_url( url_str ) + self.check_page_for_string( 'Address <b>%s</b> has been added' % address1[ 'short_desc' ] ) global regular_user regular_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() global user_address - user_address = galaxy.model.UserAddress() - user_address.user = regular_user - user_address.desc = address1[ 'short_desc' ] - user_address.name = address1[ 'name' ] - user_address.institution = address1[ 'institution' ] - user_address.address = address1[ 'address1' ]+' '+address1[ 'address2' ] - user_address.city = address1[ 'city' ] - user_address.state = address1[ 'state' ] - user_address.postal_code = address1[ 'postal_code' ] - user_address.country = address1[ 'country' ] - user_address.phone = address1[ 'phone' ] - user_address.flush() - user_address.user.refresh() + user_address = galaxy.model.UserAddress.filter( and_( galaxy.model.UserAddress.table.c.desc==address1[ 'short_desc' ], + galaxy.model.UserAddress.table.c.deleted==False ) ).first() def test_030_create_request( self ): """Testing creating, editing and submitting a request as a regular user""" # login as a regular user

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[hg] galaxy 2803: Prevent script tags in uploads as reported by ...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/88fdb7f40b0e changeset: 2803:88fdb7f40b0e user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Sep 30 09:22:02 2009 -0400 description: Prevent script tags in uploads as reported by Mitsuteru Nakao 1 file(s) affected in this change: tools/data_source/upload.py diffs (16 lines): diff -r feec758a8774 -r 88fdb7f40b0e tools/data_source/upload.py --- a/tools/data_source/upload.py Wed Sep 30 08:28:31 2009 -0400 +++ b/tools/data_source/upload.py Wed Sep 30 09:22:02 2009 -0400 @@ -49,10 +49,11 @@ regexp2 = re.compile( "<IFRAME[^>]*>", re.I ) regexp3 = re.compile( "<FRAMESET[^>]*>", re.I ) regexp4 = re.compile( "<META[^>]*>", re.I ) + regexp5 = re.compile( "<SCRIPT[^>]*>", re.I ) lineno = 0 for line in temp: lineno += 1 - matches = regexp1.search( line ) or regexp2.search( line ) or regexp3.search( line ) or regexp4.search( line ) + matches = regexp1.search( line ) or regexp2.search( line ) or regexp3.search( line ) or regexp4.search( line ) or regexp5.search( line ) if matches: if chunk is None: temp.close()

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[hg] galaxy 2804: More functional tests for Requests
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3e5428b298b1 changeset: 2804:3e5428b298b1 user: rc date: Wed Sep 30 10:40:08 2009 -0400 description: More functional tests for Requests 2 file(s) affected in this change: templates/admin/forms/show_form_read_only.mako test/functional/test_forms_and_requests.py diffs (141 lines): diff -r 88fdb7f40b0e -r 3e5428b298b1 templates/admin/forms/show_form_read_only.mako --- a/templates/admin/forms/show_form_read_only.mako Wed Sep 30 09:22:02 2009 -0400 +++ b/templates/admin/forms/show_form_read_only.mako Wed Sep 30 10:40:08 2009 -0400 @@ -62,7 +62,11 @@ </%def> <div class="toolForm"> - <div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div> + %if form.desc: + <div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div> + %else: + <div class="toolFormTitle">${form.name}</div> + %endif <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" > %if form.type == trans.app.model.FormDefinition.types.SAMPLE: %if not len(form.layout): diff -r 88fdb7f40b0e -r 3e5428b298b1 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Wed Sep 30 09:22:02 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Wed Sep 30 10:40:08 2009 -0400 @@ -169,9 +169,11 @@ #self.check_page_for_string( 'Address <b>%s</b> has been added' % user_address1[ 'short_desc' ] ) ## TODO: FIX HACK ## the user address creation should be done as a test. + global regular_user + regular_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() global user_address user_address = galaxy.model.UserAddress() - user_address.user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() + user_address.user = regular_user user_address.desc = address1[ 'short_desc' ] user_address.name = address1[ 'name' ] user_address.institution = address1[ 'institution' ] @@ -211,14 +213,22 @@ for field_value in fields: self.check_page_for_string( field_value ) # edit this request - fields = ['field one value (editted)', 'field two value (editted)', str(user_address.id)] + fields = ['field one value (edited)', 'field two value (edited)', str(user_address.id)] self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields) request_one.refresh() self.check_page_for_string( request_name+' (Renamed)' ) self.check_page_for_string( request_desc+' (Re-described)' ) + # check if the request is showing in the 'unsubmitted' filter + self.home() + self.visit_url( '%s/requests/list?show_filter=Unsubmitted' % self.url ) + self.check_page_for_string( request_one.name ) # submit the request self.submit_request( request_one.id, request_one.name ) request_one.refresh() + # check if the request is showing in the 'submitted' filter + self.home() + self.visit_url( '%s/requests/list?show_filter=Submitted' % self.url ) + self.check_page_for_string( request_one.name ) # check if the request's state is now set to 'submitted' assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.SUBMITTED ) def test_035_request_lifecycle( self ): @@ -250,40 +260,50 @@ self.visit_url('%s/requests_admin/list?show_filter=Complete' % self.url) self.check_page_for_string( request_one.name ) assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.COMPLETE ) -# def test_40_admin_create_request_on_behalf_of_regular_user( self ): -# """Testing creating and submitting a request as an admin on behalf of a regular user""" -# self.logout() -# self.login( email='test(a)bx.psu.edu' ) -## permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] -## permissions_out = [] -## self.set_library_permissions( str( library_one.id ), library_one.name, str( admin_user_private_role.id ), permissions_in, permissions_out ) -# # set field values -# fields = ['field one value', 'field two value', str(user_address.id)] -# # create the request -# request_name, request_desc = 'Request Two', 'Request Two Description' -# self.create_request_admin(request_type.id, regular_user1.id, request_name, request_desc, library_one.id, fields) -# self.check_page_for_string( request_name ) -# self.check_page_for_string( request_desc ) -# global request_two -# request_one = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name, -# galaxy.model.Request.table.c.deleted==False ) ).first() -# # check if the request's state is now set to 'unsubmitted' -# assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.UNSUBMITTED ) -# # sample fields -# samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), -# ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] -# # add samples to this request -# self.add_samples( request_two.id, request_two.name, samples ) -# for sample_name, fields in samples: -# self.check_page_for_string( sample_name ) -# self.check_page_for_string( 'Unsubmitted' ) -# for field_value in fields: -# self.check_page_for_string( field_value ) -# # submit the request -# self.submit_request( request_two.id, request_two.name ) -# request_two.refresh() -# # check if the request's state is now set to 'submitted' -# assert request_two.state is not request_two.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.SUBMITTED ) + def test_40_admin_create_request_on_behalf_of_regular_user( self ): + """Testing creating and submitting a request as an admin on behalf of a regular user""" + self.logout() + self.login( email='test(a)bx.psu.edu' ) + request_name = "RequestTwo" + # simulate request creation + url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_1=%s&field_2=%i' \ + % ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_1_value", user_address.id ) + self.home() + self.visit_url( url_str ) + self.check_page_for_string( "The new request named %s has been created" % request_name ) + global request_two + request_two = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name, + galaxy.model.Request.table.c.deleted==False ) ).first() + # check if the request is showing in the 'unsubmitted' filter + self.home() + self.visit_url( '%s/requests_admin/list?show_filter=Unsubmitted' % self.url ) + self.check_page_for_string( request_two.name ) + # check if the request's state is now set to 'unsubmitted' + assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.UNSUBMITTED ) + # sample fields + samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), + ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] + # add samples to this request + self.add_samples( request_two.id, request_two.name, samples ) + for sample_name, fields in samples: + self.check_page_for_string( sample_name ) + self.check_page_for_string( 'Unsubmitted' ) + for field_value in fields: + self.check_page_for_string( field_value ) + # submit the request + self.submit_request( request_two.id, request_two.name ) + request_two.refresh() + # check if the request is showing in the 'submitted' filter + self.home() + self.visit_url( '%s/requests_admin/list?show_filter=Submitted' % self.url ) + self.check_page_for_string( request_two.name ) + # check if the request's state is now set to 'submitted' + assert request_two.state is not request_two.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.SUBMITTED ) + # check if both the requests is showing in the 'All' filter + self.home() + self.visit_url( '%s/requests_admin/list?show_filter=All' % self.url ) + self.check_page_for_string( request_one.name ) + self.check_page_for_string( request_two.name )

1 0

[hg] galaxy 2802: Functional test fixes for uploading and sniffi...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/feec758a8774 changeset: 2802:feec758a8774 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Sep 30 08:28:31 2009 -0400 description: Functional test fixes for uploading and sniffing metadata - not sure when the behavior for these changed. 1 file(s) affected in this change: test/functional/test_sniffing_and_metadata_settings.py diffs (48 lines): diff -r 22addc979108 -r feec758a8774 test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Wed Sep 30 05:16:17 2009 -0400 +++ b/test/functional/test_sniffing_and_metadata_settings.py Wed Sep 30 08:28:31 2009 -0400 @@ -32,7 +32,7 @@ self.check_metadata_for_string( 'value="1.bed" value="\?"' ) self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) - self.check_metadata_for_string( 'Convert to new format <option value="bed">Genomic Intervals To BED <option value="gff">BED to GFF' ) + self.check_metadata_for_string( 'Convert to new format value="bed">Convert Genomic Intervals To BED <option value="gff">Convert BED to GFF' ) self.check_metadata_for_string( 'Change data type selected value="bed" selected="yes"' ) latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() @@ -97,7 +97,7 @@ self.verify_dataset_correctness( '5.gff' ) self.check_history_for_string( '5.gff format: <span class="gff">gff</span>, database: \? Info: uploaded file' ) self.check_metadata_for_string( 'value="5.gff" value="\?"' ) - self.check_metadata_for_string( 'Convert to new format <option value="bed">GFF to BED' ) + self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) self.check_metadata_for_string( 'Change data type selected value="gff" selected="yes"' ) latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() @@ -110,7 +110,7 @@ self.verify_dataset_correctness( '5.gff3' ) self.check_history_for_string( '5.gff3 format: <span class="gff3">gff3</span>, database: \? Info: uploaded file' ) self.check_metadata_for_string( 'value="5.gff3" value="\?"' ) - self.check_metadata_for_string( 'Convert to new format <option value="bed">GFF to BED' ) + self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) self.check_metadata_for_string( 'Change data type selected value="gff3" selected="yes"' ) latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() @@ -138,7 +138,7 @@ self.check_metadata_for_string( 'value="1.interval" value="\?"' ) self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) - self.check_metadata_for_string( 'Convert to new format <option value="bed">Genomic Intervals To BED' ) + self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert Genomic Intervals To BED' ) self.check_metadata_for_string( 'Change data type selected value="interval" selected="yes"' ) latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() @@ -163,7 +163,7 @@ self.verify_dataset_correctness( '3.maf' ) self.check_history_for_string( '3.maf format: <span class="maf">maf</span>, database: \? Info: uploaded file' ) self.check_metadata_for_string( 'value="3.maf" value="\?"' ) - self.check_metadata_for_string( 'Convert to new format <option value="interval">MAF to Genomic Intervals <option value="fasta">MAF to Fasta' ) + self.check_metadata_for_string( 'Convert to new format <option value="interval">Convert MAF to Genomic Intervals <option value="fasta">Convert MAF to Fasta' ) self.check_metadata_for_string( 'Change data type selected value="maf" selected="yes"' ) latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()

1 0

[hg] galaxy 2801: Refactored the library_dataset_dataset_associa...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/22addc979108 changeset: 2801:22addc979108 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Sep 30 05:16:17 2009 -0400 description: Refactored the library_dataset_dataset_association methods in the library_admin and library controllers, renamed the library_dataset controller to be library_common and moved several common methods to it, and some other code cleanup. 43 file(s) affected in this change: lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/library_admin.py lib/galaxy/web/controllers/library_common.py lib/galaxy/web/controllers/library_dataset.py templates/admin/center.mako templates/admin/library/browse_libraries.mako templates/admin/library/browse_library.mako templates/admin/library/common.mako templates/admin/library/folder_info.mako templates/admin/library/folder_permissions.mako templates/admin/library/ldda_edit_info.mako templates/admin/library/ldda_info.mako templates/admin/library/ldda_permissions.mako templates/admin/library/library_dataset_info.mako templates/admin/library/library_dataset_permissions.mako templates/admin/library/library_info.mako templates/admin/library/library_permissions.mako templates/admin/library/new_folder.mako templates/admin/library/select_info_template.mako templates/admin/library/upload.mako templates/admin/requests/show_request.mako templates/base_panels.mako templates/library/browse_libraries.mako templates/library/browse_library.mako templates/library/common.mako templates/library/folder_info.mako templates/library/folder_permissions.mako templates/library/ldda_edit_info.mako templates/library/ldda_info.mako templates/library/ldda_permissions.mako templates/library/library_dataset_common.mako templates/library/library_dataset_info.mako templates/library/library_dataset_permissions.mako templates/library/library_info.mako templates/library/library_permissions.mako templates/library/new_folder.mako templates/library/select_info_template.mako templates/library/upload.mako templates/mobile/manage_library.mako templates/requests/show_request.mako test/base/twilltestcase.py test/functional/test_forms_and_requests.py test/functional/test_security_and_libraries.py diffs (truncated from 4989 to 3000 lines): diff -r 6a066b05c94f -r 22addc979108 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue Sep 29 21:51:51 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Wed Sep 30 05:16:17 2009 -0400 @@ -3,7 +3,6 @@ from galaxy.datatypes import sniff from galaxy import util from galaxy.util.odict import odict -from galaxy.web.controllers.forms import get_all_forms from galaxy.util.streamball import StreamBall import logging, tempfile, zipfile, tarfile, os, sys @@ -94,8 +93,8 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - id = params.get( 'id', None ) - if not id: + library_id = params.get( 'obj_id', None ) + if not library_id: # To handle bots msg = "You must specify a library id." return trans.response.send_redirect( web.url_for( controller='library', @@ -103,10 +102,10 @@ default_action=params.get( 'default_action', None ), msg=util.sanitize_text( msg ), messagetype='error' ) ) - library = library=trans.app.model.Library.get( id ) + library = library=trans.app.model.Library.get( library_id ) if not library: # To handle bots - msg = "Invalid library id ( %s )." + msg = "Invalid library id ( %s )." % str( library_id ) return trans.response.send_redirect( web.url_for( controller='library', action='browse_libraries', default_action=params.get( 'default_action', None ), @@ -126,10 +125,11 @@ msg=msg, messagetype=messagetype ) @web.expose - def library( self, trans, id=None, **kwd ): + def library( self, trans, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) + library_id = params.get( 'obj_id', None ) # TODO: eventually we'll want the ability for users to create libraries if params.get( 'delete', False ): action = 'delete' @@ -137,15 +137,15 @@ action = 'permissions' else: action = 'information' - if not id: + if not library_id: msg = "You must specify a library." return trans.response.send_redirect( web.url_for( controller='library', action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='error' ) ) - library = trans.app.model.Library.get( int( id ) ) + library = trans.app.model.Library.get( int( library_id ) ) if not library: - msg = "Invalid library id ( %s ) specified." % str( id ) + msg = "Invalid library id ( %s ) specified." % str( obj_id ) return trans.response.send_redirect( web.url_for( controller='library', action='browse_libraries', msg=util.sanitize_text( msg ), @@ -175,7 +175,7 @@ msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( controller='library', action='library', - id=id, + obj_id=library.id, edit_info=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) @@ -198,7 +198,7 @@ msg = "Permissions updated for library '%s'" % library.name return trans.response.send_redirect( web.url_for( controller='library', action='library', - id=id, + obj_id=library.id, permissions=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) @@ -207,157 +207,127 @@ msg=msg, messagetype=messagetype ) @web.expose - def datasets( self, trans, library_id, ldda_ids='', **kwd ): - # This method is used by the select list labeled "Perform action on selected datasets" - # on the analysis library browser. - if not ldda_ids: - msg = "You must select at least one dataset" - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - ldda_ids = util.listify( ldda_ids ) + def folder( self, trans, obj_id, library_id, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - if not params.do_action: - msg = "You must select an action to perform on selected datasets" + if params.get( 'new', False ): + action = 'new' + elif params.get( 'delete', False ): + action = 'delete' + elif params.get( 'permissions', False ): + action = 'permissions' + else: + # 'information' will be the default + action = 'information' + folder = trans.app.model.LibraryFolder.get( int( obj_id ) ) + if not folder: + msg = "Invalid folder specified, id: %s" % str( obj_id ) return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) - if params.do_action == 'add': - history = trans.get_history() - for ldda_id in ldda_ids: - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) - hda = ldda.to_history_dataset_association( target_history=history, add_to_history = True ) - history.flush() - msg = "%i dataset(s) have been imported into your history" % len( ldda_ids ) - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - elif params.do_action == 'manage_permissions': - # We need the folder containing the LibraryDatasetDatasetAssociation(s) - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_ids[0] ) - trans.response.send_redirect( web.url_for( controller='library', - action='library_dataset_dataset_association', - library_id=library_id, - folder_id=ldda.library_dataset.folder.id, - id=','.join( ldda_ids ), - permissions=True, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) - else: - try: - if params.do_action == 'zip': - # Can't use mkstemp - the file must not exist first - tmpd = tempfile.mkdtemp() - tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) - if ziptype == '64': - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) - else: - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) - archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) - elif params.do_action == 'tgz': - archive = util.streamball.StreamBall( 'w|gz' ) - elif params.do_action == 'tbz': - archive = util.streamball.StreamBall( 'w|bz2' ) - except (OSError, zipfile.BadZipFile): - log.exception( "Unable to create archive for download" ) - msg = "Unable to create archive for download, please report this error" + user, roles = trans.get_user_and_roles() + if action == 'new': + if params.new == 'submitted': + new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ), + description=util.restore_text( params.description ) ) + # We are associating the last used genome build with folders, so we will always + # initialize a new folder with the first dbkey in util.dbnames which is currently + # ? unspecified (?) + new_folder.genome_build = util.dbnames.default_value + folder.add_folder( new_folder ) + new_folder.flush() + # New folders default to having the same permissions as their parent folder + trans.app.security_agent.copy_library_permissions( folder, new_folder ) + msg = "New folder named '%s' has been added to the library" % new_folder.name return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), - messagetype='error' ) ) - seen = [] - user, roles = trans.get_user_and_roles() - for id in ldda_ids: - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda or not trans.app.security_agent.can_access_dataset( roles, ldda.dataset ): - continue - path = "" - parent_folder = ldda.library_dataset.folder - while parent_folder is not None: - # Exclude the now-hidden "root folder" - if parent_folder.parent is None: - path = os.path.join( parent_folder.library_root[0].name, path ) - break - path = os.path.join( parent_folder.name, path ) - parent_folder = parent_folder.parent - path += ldda.name - while path in seen: - path += '_' - seen.append( path ) - try: - archive.add( ldda.dataset.file_name, path ) - except IOError: - log.exception( "Unable to write to temporary library download archive" ) - msg = "Unable to create archive for download, please report this error" + messagetype='done' ) ) + return trans.fill_template( '/library/new_folder.mako', + library_id=library_id, + folder=folder, + msg=msg, + messagetype=messagetype ) + elif action == 'information': + # See if we have any associated templates + widgets = folder.get_template_widgets( trans ) + if params.get( 'rename_folder_button', False ): + if trans.app.security_agent.can_modify_library_item( user, roles, folder ): + old_name = folder.name + new_name = util.restore_text( params.name ) + new_description = util.restore_text( params.description ) + if not new_name: + msg = 'Enter a valid name' + return trans.fill_template( "/library/folder_info.mako", + folder=folder, + library_id=library_id, + widgets=widgets, + msg=msg, + messagetype='error' ) + else: + folder.name = new_name + folder.description = new_description + folder.flush() + msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( controller='library', + action='folder', + obj_id=folder.id, + library_id=library_id, + rename=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + else: + msg = "You are not authorized to edit this folder" + return trans.fill_template( "/library/folder_info.mako", + folder=folder, + library_id=library_id, + widgets=widgets, + msg=msg, + messagetype='error' ) + return trans.fill_template( '/library/folder_info.mako', + folder=folder, + library_id=library_id, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif action == 'permissions': + if params.get( 'update_roles_button', False ): + # The user clicked the Save button on the 'Associate With Roles' form + if trans.app.security_agent.can_manage_library_item( user, roles, folder ): + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + trans.app.security_agent.set_all_library_permissions( folder, permissions ) + folder.refresh() + msg = 'Permissions updated for folder %s' % folder.name return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, + action='folder', + obj_id=folder.id, + library_id=library_id, + permissions=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + else: + msg = "You are not authorized to manage permissions on this folder" + return trans.response.send_redirect( web.url_for( controller='library', + action='folder', + obj_id=folder.id, + library_id=library_id, + permissions=True, msg=util.sanitize_text( msg ), messagetype='error' ) ) - if params.do_action == 'zip': - archive.close() - tmpfh = open( tmpf ) - # clean up now - try: - os.unlink( tmpf ) - os.rmdir( tmpd ) - except OSError: - log.exception( "Unable to remove temporary library download archive and directory" ) - msg = "Unable to create archive for download, please report this error" - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - trans.response.set_content_type( "application/x-zip-compressed" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action - return tmpfh - else: - trans.response.set_content_type( "application/x-tar" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action - archive.wsgi_status = trans.response.wsgi_status() - archive.wsgi_headeritems = trans.response.wsgi_headeritems() - return archive.stream + return trans.fill_template( '/library/folder_permissions.mako', + folder=folder, + library_id=library_id, + msg=msg, + messagetype=messagetype ) @web.expose - def download_dataset_from_folder(self, trans, id, library_id=None, **kwd): - """Catches the dataset id and displays file contents as directed""" - # id must refer to a LibraryDatasetDatasetAssociation object - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( id ) - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=msg, - messagetype='error' ) ) - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) - trans.response.set_content_type( mime ) - fStat = os.stat( ldda.file_name ) - trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = ldda.name - fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( id ), fname ) - try: - return open( ldda.file_name ) - except: - msg = 'This dataset contains no content' - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=msg, - messagetype='error' ) ) - @web.expose - def library_dataset( self, trans, id, library_id, **kwd ): + def library_dataset( self, trans, obj_id, library_id, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -365,12 +335,12 @@ action = 'permissions' else: action = 'information' - library_dataset = trans.app.model.LibraryDataset.get( id ) + library_dataset = trans.app.model.LibraryDataset.get( obj_id ) if not library_dataset: - msg = "Invalid library dataset specified, id: %s" %str( id ) + msg = "Invalid library dataset specified, id: %s" %str( obj_id ) return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) user, roles = trans.get_user_and_roles() @@ -424,7 +394,248 @@ msg=msg, messagetype=messagetype ) @web.expose - def library_dataset_dataset_association( self, trans, library_id, folder_id, id=None, **kwd ): + def ldda_edit_info( self, trans, library_id, folder_id, obj_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if not ldda: + msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id ) + return trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + dbkey = params.get( 'dbkey', '?' ) + if isinstance( dbkey, list ): + dbkey = dbkey[0] + user, roles = trans.get_user_and_roles() + file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] + file_formats.sort() + # See if we have any associated templates + widgets = ldda.get_template_widgets( trans ) + if params.get( 'change', False ): + # The user clicked the Save button on the 'Change data type' form + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): + if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: + trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) + trans.app.model.flush() + msg = "Data type changed for library dataset '%s'" % ldda.name + messagetype = 'done' + else: + msg = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) + messagetype = 'error' + else: + msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name + messagetype = 'error' + return trans.fill_template( "/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif params.get( 'save', False ): + # The user clicked the Save button on the 'Edit Attributes' form + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): + old_name = ldda.name + new_name = util.restore_text( params.get( 'name', '' ) ) + new_info = util.restore_text( params.get( 'info', '' ) ) + new_message = util.restore_text( params.get( 'message', '' ) ) + if not new_name: + msg = 'Enter a valid name' + messagetype = 'error' + else: + ldda.name = new_name + ldda.info = new_info + ldda.message = new_message + # The following for loop will save all metadata_spec items + for name, spec in ldda.datatype.metadata_spec.items(): + if spec.get("readonly"): + continue + optional = params.get( "is_" + name, None ) + if optional and optional == 'true': + # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) + setattr( ldda.metadata, name, None ) + else: + setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) + ldda.metadata.dbkey = dbkey + ldda.datatype.after_edit( ldda ) + trans.app.model.flush() + msg = 'Attributes updated for library dataset %s' % ldda.name + messagetype = 'done' + else: + msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name + messagetype = 'error' + return trans.fill_template( "/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif params.get( 'detect', False ): + # The user clicked the Auto-detect button on the 'Edit Attributes' form + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): + for name, spec in ldda.datatype.metadata_spec.items(): + # We need to be careful about the attributes we are resetting + if name not in [ 'name', 'info', 'dbkey' ]: + if spec.get( 'default' ): + setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) + ldda.datatype.set_meta( ldda ) + ldda.datatype.after_edit( ldda ) + trans.app.model.flush() + msg = 'Attributes updated for library dataset %s' % ldda.name + messagetype = 'done' + else: + msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name + messagetype = 'error' + return trans.fill_template( "/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif params.get( 'delete', False ): + if trans.app.security_agent.can_modify_library_item( user, roles, folder ): + ldda.deleted = True + ldda.flush() + msg = 'Dataset %s has been removed from this data library' % ldda.name + messagetype = 'done' + else: + msg = "you are not authorized to delete dataset '%s'" % ldda.name + messagetype = 'error' + return trans.fill_template( "/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): + ldda.datatype.before_edit( ldda ) + if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: + # Copy dbkey into metadata, for backwards compatability + # This looks like it does nothing, but getting the dbkey + # returns the metadata dbkey unless it is None, in which + # case it resorts to the old dbkey. Setting the dbkey + # sets it properly in the metadata + ldda.metadata.dbkey = ldda.dbkey + return trans.fill_template( "/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + @web.expose + def ldda_display_info( self, trans, library_id, folder_id, obj_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if not ldda: + msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( obj_id ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + # See if we have any associated templates + widgets = ldda.get_template_widgets( trans ) + return trans.fill_template( '/library/ldda_info.mako', + ldda=ldda, + library_id=library_id, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + @web.expose + def ldda_manage_permissions( self, trans, library_id, folder_id, obj_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + obj_ids = util.listify( obj_id ) + # Display permission form, permissions will be updated for all lddas simultaneously. + lddas = [] + for obj_id in [ int( obj_id ) for obj_id in obj_ids ]: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if ldda is None: + msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( obj_id ) + trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + lddas.append( ldda ) + if params.get( 'update_roles_button', False ): + if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ + trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): + permissions = {} + for k, v in trans.app.model.Dataset.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + for ldda in lddas: + # Set the DATASET permissions on the Dataset + trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) + ldda.dataset.refresh() + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + for ldda in lddas: + # Set the LIBRARY permissions on the LibraryDataset + # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions + trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) + ldda.library_dataset.refresh() + # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation + trans.app.security_agent.set_all_library_permissions( ldda, permissions ) + ldda.refresh() + msg = 'Permissions and roles have been updated on %d datasets' % len( lddas ) + messagetype = 'done' + else: + msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name + messagetype = 'error' + return trans.fill_template( "/library/ldda_permissions.mako", + ldda=lddas, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ + trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): + # Ensure that the permissions across all library items are identical, otherwise we can't update them together. + check_list = [] + for ldda in lddas: + permissions = [] + # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation + # will always be the same as the permissions on the associated LibraryDataset, so we only need to + # check one Library object + for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): + if library_permission.action not in permissions: + permissions.append( library_permission.action ) + for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): + if dataset_permission.action not in permissions: + permissions.append( dataset_permission.action ) + permissions.sort() + if not check_list: + check_list = permissions + if permissions != check_list: + msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' + trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + else: + msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name + messagetype = 'error' + return trans.fill_template( "/library/ldda_permissions.mako", + ldda=lddas, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + @web.expose + def upload_library_dataset( self, trans, library_id, folder_id, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -444,279 +655,6 @@ else: replace_dataset = None user, roles = trans.get_user_and_roles() - # Let's not overwrite the imported datatypes module with the variable datatypes? - # The built-in 'id' is overwritten in lots of places as well - ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] - ldatatypes.sort() - if id: - if params.get( 'permissions', False ): - action = 'permissions' - elif params.get( 'edit_info', False ): - action = 'edit_info' - else: - action = 'info' - if id.count( ',' ): - ids = id.split( ',' ) - id = None - else: - ids = None - else: - ids = None - if id: - # ldda_id specified, display attributes form - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda: - msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - # See if we have any associated templates - widgets = ldda.get_template_widgets( trans ) - if action == 'permissions': - if params.get( 'update_roles_button', False ): - # The user clicked the Save button on the 'Associate With Roles' form - if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ - trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): - permissions = {} - for k, v in trans.app.model.Dataset.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - # Set the DATASET permissions on the Dataset - trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) - ldda.dataset.refresh() - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) - ldda.library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( ldda, permissions ) - ldda.refresh() - msg = "Permissions updated for dataset '%s'" % ldda.name - messagetype = 'done' - else: - msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( '/library/ldda_permissions.mako', - ldda=ldda, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - elif action == 'info': - return trans.fill_template( '/library/ldda_info.mako', - ldda=ldda, - library_id=library_id, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif action == 'edit_info': - if params.get( 'change', False ): - # The user clicked the Save button on the 'Change data type' form - if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): - if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: - trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() - msg = "Data type changed for library dataset '%s'" % ldda.name - messagetype = 'done' - else: - msg = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) - messagetype = 'error' - else: - msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( "/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif params.get( 'save', False ): - # The user clicked the Save button on the 'Edit Attributes' form - if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): - old_name = ldda.name - new_name = util.restore_text( params.get( 'name', '' ) ) - new_info = util.restore_text( params.get( 'info', '' ) ) - new_message = util.restore_text( params.get( 'message', '' ) ) - if not new_name: - msg = 'Enter a valid name' - messagetype = 'error' - else: - ldda.name = new_name - ldda.info = new_info - ldda.message = new_message - # The following for loop will save all metadata_spec items - for name, spec in ldda.datatype.metadata_spec.items(): - if spec.get("readonly"): - continue - optional = params.get( "is_" + name, None ) - if optional and optional == 'true': - # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( ldda.metadata, name, None ) - else: - setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) - ldda.metadata.dbkey = dbkey - ldda.datatype.after_edit( ldda ) - trans.app.model.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' - else: - msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( "/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif params.get( 'detect', False ): - # The user clicked the Auto-detect button on the 'Edit Attributes' form - if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): - for name, spec in ldda.datatype.metadata_spec.items(): - # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: - if spec.get( 'default' ): - setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - ldda.datatype.set_meta( ldda ) - ldda.datatype.after_edit( ldda ) - trans.app.model.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' - else: - msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( "/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif params.get( 'delete', False ): - if trans.app.security_agent.can_modify_library_item( user, roles, folder ): - ldda.deleted = True - ldda.flush() - msg = 'Dataset %s has been removed from this library' % ldda.name - messagetype = 'done' - else: - msg = "you are not authorized to delete dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( "/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): - ldda.datatype.before_edit( ldda ) - if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: - # Copy dbkey into metadata, for backwards compatability - # This looks like it does nothing, but getting the dbkey - # returns the metadata dbkey unless it is None, in which - # case it resorts to the old dbkey. Setting the dbkey - # sets it properly in the metadata - ldda.metadata.dbkey = ldda.dbkey - return trans.fill_template( "/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif ids: - # Multiple ids specified, display permission form, permissions will be updated for all simultaneously. - lddas = [] - for id in [ int( id ) for id in ids ]: - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if ldda is None: - msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) - trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - lddas.append( ldda ) - if len( lddas ) < 2: - msg = 'You must specify at least two datasets on which to modify permissions, ids you sent: %s' % str( ids ) - trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - if action == 'permissions': - if params.get( 'update_roles_button', False ): - if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ - trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): - permissions = {} - for k, v in trans.app.model.Dataset.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the DATASET permissions on the Dataset - trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) - ldda.dataset.refresh() - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) - ldda.library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( ldda, permissions ) - ldda.refresh() - msg = 'Permissions and roles have been updated on %d datasets' % len( lddas ) - messagetype = 'done' - else: - msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( "/library/ldda_permissions.mako", - ldda=lddas, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ - trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): - # Ensure that the permissions across all library items are identical, otherwise we can't update them together. - check_list = [] - for ldda in lddas: - permissions = [] - # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation - # will always be the same as the permissions on the associated LibraryDataset, so we only need to - # check one Library object - for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): - if library_permission.action not in permissions: - permissions.append( library_permission.action ) - for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): - if dataset_permission.action not in permissions: - permissions.append( dataset_permission.action ) - permissions.sort() - if not check_list: - check_list = permissions - if permissions != check_list: - msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' - trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - else: - msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( "/library/ldda_permissions.mako", - ldda=lddas, - library_id=library_id, - msg=msg, - messagetype=messagetype ) if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \ ( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ): if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ): @@ -729,7 +667,7 @@ template_id = 'None' widgets = [] upload_option = params.get( 'upload_option', 'upload_file' ) - created_outputs = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans, + created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, controller='library', library_id=library_id, folder_id=folder_id, @@ -761,7 +699,7 @@ default_action = 'add' trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, default_action=default_action, created_ldda_ids=",".join( ldda_id_list ), msg=util.sanitize_text( msg ), @@ -771,45 +709,44 @@ msg = "Upload failed" trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, created_ldda_ids=",".join( ldda_id_list ), msg=util.sanitize_text( msg ), messagetype='error' ) ) - if not id or replace_dataset: - # See if we have any inherited templates, but do not inherit contents. - widgets = folder.get_template_widgets( trans, get_contents=False ) - upload_option = params.get( 'upload_option', 'upload_file' ) - # No dataset(s) specified, so display the upload form. Send list of data formats to the form - # so the "extension" select list can be populated dynamically - file_formats = trans.app.datatypes_registry.upload_file_formats - # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically - def get_dbkey_options( last_used_build ): - for dbkey, build_name in util.dbnames: - yield build_name, dbkey, ( dbkey==last_used_build ) - dbkeys = get_dbkey_options( last_used_build ) - # Send list of roles to the form so the dataset can be associated with 1 or more of them. - roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() - # Send the current history to the form to enable importing datasets from history to library - history = trans.get_history() - history.refresh() - # If we're using nginx upload, override the form action - action = web.url_for( controller='library', action='library_dataset_dataset_association' ) - if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: - action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action - return trans.fill_template( '/library/upload.mako', - upload_option=upload_option, - action=action, - library_id=library_id, - folder_id=folder_id, - replace_dataset=replace_dataset, - file_formats=file_formats, - dbkeys=dbkeys, - last_used_build=last_used_build, - roles=roles, - history=history, - widgets=widgets, - msg=msg, - messagetype=messagetype ) + # See if we have any inherited templates, but do not inherit contents. + widgets = folder.get_template_widgets( trans, get_contents=False ) + upload_option = params.get( 'upload_option', 'upload_file' ) + # No dataset(s) specified, so display the upload form. Send list of data formats to the form + # so the "extension" select list can be populated dynamically + file_formats = trans.app.datatypes_registry.upload_file_formats + # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically + def get_dbkey_options( last_used_build ): + for dbkey, build_name in util.dbnames: + yield build_name, dbkey, ( dbkey==last_used_build ) + dbkeys = get_dbkey_options( last_used_build ) + # Send list of roles to the form so the dataset can be associated with 1 or more of them. + roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() + # Send the current history to the form to enable importing datasets from history to library + history = trans.get_history() + history.refresh() + # If we're using nginx upload, override the form action + action = web.url_for( controller='library', action='upload_library_dataset' ) + if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: + action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action + return trans.fill_template( '/library/upload.mako', + upload_option=upload_option, + action=action, + library_id=library_id, + folder_id=folder_id, + replace_dataset=replace_dataset, + file_formats=file_formats, + dbkeys=dbkeys, + last_used_build=last_used_build, + roles=roles, + history=history, + widgets=widgets, + msg=msg, + messagetype=messagetype ) @web.expose def add_history_datasets_to_library( self, trans, library_id, folder_id, hda_ids='', **kwd ): params = util.Params( kwd ) @@ -821,7 +758,7 @@ msg = "Invalid folder id: %s" % str( folder_id ) return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) replace_id = params.get( 'replace_id', None ) @@ -836,7 +773,7 @@ msg = 'Your current history is empty' return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) if params.get( 'add_history_datasets_to_library_button', False ): @@ -861,7 +798,7 @@ msg = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id ) return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) if created_ldda_ids: @@ -890,7 +827,7 @@ default_action = 'add' return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, created_ldda_ids=created_ldda_ids.lstrip( ',' ), default_action=default_action, msg=util.sanitize_text( msg ), @@ -923,264 +860,152 @@ msg=msg, messagetype=messagetype ) @web.expose - def folder( self, trans, id, library_id, **kwd ): + def download_dataset_from_folder(self, trans, obj_id, library_id=None, **kwd): + """Catches the dataset id and displays file contents as directed""" + # id must refer to a LibraryDatasetDatasetAssociation object + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if not ldda.dataset: + msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id ) + return trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=msg, + messagetype='error' ) ) + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) + trans.response.set_content_type( mime ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname ) + try: + return open( ldda.file_name ) + except: + msg = 'This dataset contains no content' + return trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=msg, + messagetype='error' ) ) + @web.expose + def datasets( self, trans, library_id, ldda_ids='', **kwd ): + # This method is used by the select list labeled "Perform action on selected datasets" + # on the analysis library browser. + if not ldda_ids: + msg = "You must select at least one dataset" + return trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + ldda_ids = util.listify( ldda_ids ) params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - if params.get( 'new', False ): - action = 'new' - elif params.get( 'delete', False ): - action = 'delete' - elif params.get( 'permissions', False ): - action = 'permissions' - else: - # 'information' will be the default - action = 'information' - folder = trans.app.model.LibraryFolder.get( int( id ) ) - if not folder: - msg = "Invalid folder specified, id: %s" % str( id ) + if not params.do_action: + msg = "You must select an action to perform on selected datasets" return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) - user, roles = trans.get_user_and_roles() - if action == 'new': - if params.new == 'submitted': - new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ), - description=util.restore_text( params.description ) ) - # We are associating the last used genome build with folders, so we will always - # initialize a new folder with the first dbkey in util.dbnames which is currently - # ? unspecified (?) - new_folder.genome_build = util.dbnames.default_value - folder.add_folder( new_folder ) - new_folder.flush() - # New folders default to having the same permissions as their parent folder - trans.app.security_agent.copy_library_permissions( folder, new_folder ) - msg = "New folder named '%s' has been added to the library" % new_folder.name + if params.do_action == 'add': + history = trans.get_history() + for ldda_id in ldda_ids: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) + hda = ldda.to_history_dataset_association( target_history=history, add_to_history = True ) + history.flush() + msg = "%i dataset(s) have been imported into your history" % len( ldda_ids ) + return trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + elif params.do_action == 'manage_permissions': + # We need the folder containing the LibraryDatasetDatasetAssociation(s) + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_ids[0] ) + trans.response.send_redirect( web.url_for( controller='library', + action='upload_library_dataset', + library_id=library_id, + folder_id=ldda.library_dataset.folder.id, + obj_id=','.join( ldda_ids ), + permissions=True, + msg=util.sanitize_text( msg ), + messagetype=messagetype ) ) + else: + try: + if params.do_action == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) + if ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif params.do_action == 'tgz': + archive = util.streamball.StreamBall( 'w|gz' ) + elif params.do_action == 'tbz': + archive = util.streamball.StreamBall( 'w|bz2' ) + except (OSError, zipfile.BadZipFile): + log.exception( "Unable to create archive for download" ) + msg = "Unable to create archive for download, please report this error" return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/library/new_folder.mako', - library_id=library_id, - folder=folder, - msg=msg, - messagetype=messagetype ) - elif action == 'information': - # See if we have any associated templates - widgets = folder.get_template_widgets( trans ) - if params.get( 'rename_folder_button', False ): - if trans.app.security_agent.can_modify_library_item( user, roles, folder ): - old_name = folder.name - new_name = util.restore_text( params.name ) - new_description = util.restore_text( params.description ) - if not new_name: - msg = 'Enter a valid name' - return trans.fill_template( "/library/folder_info.mako", - folder=folder, - library_id=library_id, - widgets=widgets, - msg=msg, - messagetype='error' ) - else: - folder.name = new_name - folder.description = new_description - folder.flush() - msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( controller='library', - action='folder', - id=id, - library_id=library_id, - rename=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - else: - msg = "You are not authorized to edit this folder" - return trans.fill_template( "/library/folder_info.mako", - folder=folder, - library_id=library_id, - widgets=widgets, - msg=msg, - messagetype='error' ) - return trans.fill_template( '/library/folder_info.mako', - folder=folder, - library_id=library_id, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif action == 'permissions': - if params.get( 'update_roles_button', False ): - # The user clicked the Save button on the 'Associate With Roles' form - if trans.app.security_agent.can_manage_library_item( user, roles, folder ): - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( folder, permissions ) - folder.refresh() - msg = 'Permissions updated for folder %s' % folder.name + messagetype='error' ) ) + seen = [] + user, roles = trans.get_user_and_roles() + for ldda_id in ldda_ids: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) + if not ldda or not trans.app.security_agent.can_access_dataset( roles, ldda.dataset ): + continue + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + try: + archive.add( ldda.dataset.file_name, path ) + except IOError: + log.exception( "Unable to write to temporary library download archive" ) + msg = "Unable to create archive for download, please report this error" return trans.response.send_redirect( web.url_for( controller='library', - action='folder', - id=id, - library_id=library_id, - permissions=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - else: - msg = "You are not authorized to manage permissions on this folder" - return trans.response.send_redirect( web.url_for( controller='library', - action='folder', - id=id, - library_id=library_id, - permissions=True, + action='browse_library', + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) - return trans.fill_template( '/library/folder_permissions.mako', - folder=folder, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - @web.expose - def info_template( self, trans, library_id, id=None, folder_id=None, ldda_id=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if id: - library_item = trans.app.model.FormDefinition.get( int( id ) ) - library_item_desc = 'information template' - response_action = 'info_template' - response_id = id - elif folder_id: - library_item = trans.app.model.LibraryFolder.get( int( folder_id ) ) - library_item_desc = 'folder' - response_action = 'folder' - response_id = folder_id - elif ldda_id: - library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_id ) ) - library_item_desc = 'library dataset' - response_action = 'library_dataset_dataset_association' - response_id = ldda_id - else: - library_item = trans.app.model.Library.get( int( library_id ) ) - library_item_desc = 'library' - response_action = 'browse_library' - response_id = library_id - forms = get_all_forms( trans, - filter=dict( deleted=False ), - form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) - if not forms: - msg = "There are no forms on which to base the template, so create a form and " - msg += "try again to add the information template to the %s." % library_item_desc - trans.response.send_redirect( web.url_for( controller='forms', - action='new', - new=True, - msg=msg, - messagetype='done' ) ) - if params.get( 'add', False ): - if params.get( 'add_info_template_button', False ): - form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) ) - #fields = list( copy.deepcopy( form.fields ) ) - form_values = trans.app.model.FormValues( form, [] ) - form_values.flush() - if folder_id: - assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values ) - elif ldda_id: - assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values ) - else: - assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values ) - assoc.flush() - msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) - trans.response.send_redirect( web.url_for( controller='library', - action=response_action, - id=response_id, - msg=msg, - message_type='done' ) ) - return trans.fill_template( '/admin/library/select_info_template.mako', - library_item_name=library_item.name, - library_item_desc=library_item_desc, - library_id=library_id, - folder_id=folder_id, - ldda_id=ldda_id, - forms=forms, - msg=msg, - messagetype=messagetype ) - @web.expose - def edit_template_info( self, trans, library_id, num_widgets, library_item_id=None, library_item_type=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - folder_id = None - if library_item_type == 'library': - library_item = trans.app.model.Library.get( library_item_id ) - elif library_item_type == 'library_dataset': - library_item = trans.app.model.LibraryDataset.get( library_item_id ) - elif library_item_type == 'folder': - library_item = trans.app.model.LibraryFolder.get( library_item_id ) - elif library_item_type == 'library_dataset_dataset_association': - library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id ) - # This response_action method requires a folder_id - folder_id = library_item.library_dataset.folder.id - else: - msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) ) - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - # Save updated template field contents - field_values = [] - for index in range( int( num_widgets ) ): - field_values.append( util.restore_text( params.get( 'field_%i' % ( index ), '' ) ) ) - info = library_item.info_association[0].info - form_values = trans.app.model.FormValues.get( info.id ) - form_values.content = field_values - form_values.flush() - msg = 'The information has been updated.' - return trans.response.send_redirect( web.url_for( controller='library', - action=library_item_type, - id=library_item.id, - library_id=library_id, - folder_id=folder_id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - -# ---- Utility methods ------------------------------------------------------- - -def active_folders( trans, folder ): - # Much faster way of retrieving all active sub-folders within a given folder than the - # performance of the mapper. This query also eagerloads the permissions on each folder. - return trans.sa_session.query( trans.app.model.LibraryFolder ) \ - .filter_by( parent=folder, deleted=False ) \ - .options( eagerload_all( "actions" ) ) \ - .order_by( trans.app.model.LibraryFolder.table.c.name ) \ - .all() -def activatable_folders( trans, folder ): - return trans.sa_session.query( trans.app.model.LibraryFolder ) \ - .filter_by( parent=folder, purged=False ) \ - .options( eagerload_all( "actions" ) ) \ - .order_by( trans.app.model.LibraryFolder.table.c.name ) \ - .all() -def active_folders_and_lddas( trans, folder ): - folders = active_folders( trans, folder ) - # This query is much faster than the folder.active_library_datasets property - lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \ - .filter_by( deleted=False ) \ - .join( "library_dataset" ) \ - .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \ - .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \ - .all() - return folders, lddas -def activatable_folders_and_lddas( trans, folder ): - folders = activatable_folders( trans, folder ) - # This query is much faster than the folder.activatable_library_datasets property - lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \ - .join( "library_dataset" ) \ - .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \ - .join( "dataset" ) \ - .filter( trans.app.model.Dataset.table.c.deleted==False ) \ - .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \ - .all() - return folders, lddas + if params.do_action == 'zip': + archive.close() + tmpfh = open( tmpf ) + # clean up now + try: + os.unlink( tmpf ) + os.rmdir( tmpd ) + except OSError: + log.exception( "Unable to remove temporary library download archive and directory" ) + msg = "Unable to create archive for download, please report this error" + return trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + trans.response.set_content_type( "application/x-zip-compressed" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action + return tmpfh + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream diff -r 6a066b05c94f -r 22addc979108 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Sep 29 21:51:51 2009 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Wed Sep 30 05:16:17 2009 -0400 @@ -2,7 +2,6 @@ from galaxy import util from galaxy.web.base.controller import * from galaxy.model.orm import * -from galaxy.web.controllers.forms import get_all_forms # Older py compatibility try: set() @@ -32,18 +31,19 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - id = params.get( 'id', None ) - deleted = util.string_as_bool( params.get( 'deleted', False ) ) - show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) - if not id: + library_id = params.get( 'obj_id', None ) + if not library_id: + # To handle bots msg = "You must specify a library id." return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='error' ) ) - library = library=trans.app.model.Library.get( id ) + deleted = util.string_as_bool( params.get( 'deleted', False ) ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + library = library=trans.app.model.Library.get( library_id ) if not library: - msg = "Invalid library id ( %s )." + msg = "Invalid library id ( %s )." % str( library_id ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', msg=util.sanitize_text( msg ), @@ -55,17 +55,17 @@ return trans.fill_template( '/admin/library/browse_library.mako', library=library, deleted=deleted, + show_deleted=show_deleted, created_ldda_ids=created_ldda_ids, - forms=get_all_forms( trans, filter=dict(deleted=False) ), msg=msg, - messagetype=messagetype, - show_deleted=show_deleted ) + messagetype=messagetype ) @web.expose @web.require_admin - def library( self, trans, id=None, **kwd ): + def library( self, trans, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) + library_id = params.get( 'obj_id', None ) if params.get( 'new', False ): action = 'new' elif params.get( 'delete', False ): @@ -74,14 +74,14 @@ action = 'permissions' else: action = 'information' - if not id and not action == 'new': + if not library_id and not action == 'new': msg = "You must specify a library to %s." % action return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='error' ) ) if not action == 'new': - library = trans.app.model.Library.get( int( id ) ) + library = trans.app.model.Library.get( int( library_id ) ) if action == 'new': if params.new == 'submitted': library = trans.app.model.Library( name = util.restore_text( params.name ), @@ -93,7 +93,7 @@ msg = "The new library named '%s' has been created" % library.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library.id, + obj_id=library.id, msg=util.sanitize_text( msg ), messagetype='done' ) ) return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype ) @@ -122,7 +122,7 @@ msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='library', - id=id, + obj_id=library.id, edit_info=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) @@ -171,7 +171,7 @@ msg = "Permissions updated for library '%s'" % library.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='library', - id=id, + obj_id=library.id, permissions=True, msg=util.sanitize_text( msg ), messagetype='done' ) ) @@ -198,7 +198,7 @@ @web.require_admin def purge_library( self, trans, **kwd ): params = util.Params( kwd ) - library = trans.app.model.Library.get( int( params.id ) ) + library = trans.app.model.Library.get( int( params.obj_id ) ) def purge_folder( library_folder ): for lf in library_folder.folders: purge_folder( lf ) @@ -240,7 +240,7 @@ messagetype='done' ) ) @web.expose @web.require_admin - def folder( self, trans, id, library_id, **kwd ): + def folder( self, trans, obj_id, library_id, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -253,12 +253,12 @@ else: # 'information' will be the default action = 'information' - folder = trans.app.model.LibraryFolder.get( int( id ) ) + folder = trans.app.model.LibraryFolder.get( int( obj_id ) ) if not folder: - msg = "Invalid folder specified, id: %s" % str( id ) + msg = "Invalid folder specified, id: %s" % str( obj_id ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) if action == 'new': @@ -276,7 +276,7 @@ msg = "New folder named '%s' has been added to the library" % new_folder.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='done' ) ) return trans.fill_template( '/admin/library/new_folder.mako', @@ -306,7 +306,7 @@ msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='folder', - id=id, + obj_id=folder.id, library_id=library_id, edit_info=True, msg=util.sanitize_text( msg ), @@ -322,7 +322,7 @@ folder.flush() msg = "Folder '%s' and all of its contents have been marked deleted" % folder.name return trans.response.send_redirect( web.url_for( action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='done' ) ) elif action =='permissions': @@ -337,7 +337,7 @@ msg = "Permissions updated for folder '%s'" % folder.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='folder', - id=id, + obj_id=folder.id, library_id=library_id, permissions=True, msg=util.sanitize_text( msg ), @@ -349,7 +349,7 @@ messagetype=messagetype ) @web.expose @web.require_admin - def library_dataset( self, trans, id, library_id, **kwd ): + def library_dataset( self, trans, obj_id, library_id, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -357,12 +357,12 @@ action = 'permissions' else: action = 'information' - library_dataset = trans.app.model.LibraryDataset.get( id ) + library_dataset = trans.app.model.LibraryDataset.get( obj_id ) if not library_dataset: - msg = "Invalid library dataset specified, id: %s" %str( id ) + msg = "Invalid library dataset specified, id: %s" %str( obj_id ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) if action == 'information': @@ -406,13 +406,261 @@ messagetype=messagetype ) @web.expose @web.require_admin - def library_dataset_dataset_association( self, trans, library_id, folder_id, id=None, **kwd ): + def ldda_edit_info( self, trans, library_id, folder_id, obj_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if not ldda: + msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + dbkey = params.get( 'dbkey', '?' ) + if isinstance( dbkey, list ): + dbkey = dbkey[0] + file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] + file_formats.sort() + # See if we have any associated templates + widgets = ldda.get_template_widgets( trans ) + if params.get( 'change', False ): + # The user clicked the Save button on the 'Change data type' form + if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: + trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) + trans.app.model.flush() + msg = "Data type changed for library dataset '%s'" % ldda.name + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + else: + return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % \ + ( ldda.extension, params.datatype ) ) + elif params.get( 'save', False ): + # The user clicked the Save button on the 'Edit Attributes' form + old_name = ldda.name + new_name = util.restore_text( params.get( 'name', '' ) ) + new_info = util.restore_text( params.get( 'info', '' ) ) + new_message = util.restore_text( params.get( 'message', '' ) ) + if not new_name: + msg = 'Enter a valid name' + messagetype = 'error' + else: + ldda.name = new_name + ldda.info = new_info + ldda.message = new_message + # The following for loop will save all metadata_spec items + for name, spec in ldda.datatype.metadata_spec.items(): + if spec.get("readonly"): + continue + optional = params.get( "is_" + name, None ) + if optional and optional == 'true': + # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) + setattr( ldda.metadata, name, None ) + else: + setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) + ldda.metadata.dbkey = dbkey + ldda.datatype.after_edit( ldda ) + trans.app.model.flush() + msg = 'Attributes updated for library dataset %s' % ldda.name + messagetype = 'done' + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif params.get( 'detect', False ): + # The user clicked the Auto-detect button on the 'Edit Attributes' form + for name, spec in ldda.datatype.metadata_spec.items(): + # We need to be careful about the attributes we are resetting + if name not in [ 'name', 'info', 'dbkey' ]: + if spec.get( 'default' ): + setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) + ldda.datatype.set_meta( ldda ) + ldda.datatype.after_edit( ldda ) + trans.app.model.flush() + msg = 'Attributes updated for library dataset %s' % ldda.name + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif params.get( 'delete', False ): + ldda.deleted = True + ldda.flush() + msg = 'Dataset %s has been removed from this data library' % ldda.name + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + ldda.datatype.before_edit( ldda ) + if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: + # Copy dbkey into metadata, for backwards compatability + # This looks like it does nothing, but getting the dbkey + # returns the metadata dbkey unless it is None, in which + # case it resorts to the old dbkey. Setting the dbkey + # sets it properly in the metadata + ldda.metadata.dbkey = ldda.dbkey + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + file_formats=file_formats, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def ldda_display_info( self, trans, library_id, folder_id, obj_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if not ldda: + msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + # See if we have any associated templates + widgets = ldda.get_template_widgets( trans ) + return trans.fill_template( '/admin/library/ldda_info.mako', + ldda=ldda, + library_id=library_id, + show_deleted=show_deleted, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def ldda_manage_permissions( self, trans, library_id, folder_id, obj_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + obj_ids = util.listify( obj_id ) + # Display permission form, permissions will be updated for all lddas simultaneously. + lddas = [] + for obj_id in [ int( obj_id ) for obj_id in obj_ids ]: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if ldda is None: + msg = 'You specified an invalid LibraryDatasetDatasetAssociation obj_id: %s' %str( obj_id ) + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + lddas.append( ldda ) + if params.get( 'update_roles_button', False ): + permissions = {} + accessible = False + for k, v in trans.app.model.Dataset.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] + # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible + if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + if len( in_roles ) > 1: + # Get the set of all users that are being associated with the dataset + in_roles_set = set() + for role in in_roles: + in_roles_set.add( role ) + users_set = set() + for role in in_roles: + for ura in role.users: + users_set.add( ura.user ) + # Make sure that at least 1 user has every role being associated with the dataset + for user in users_set: + user_roles_set = set() + for ura in user.roles: + user_roles_set.add( ura.role ) + if in_roles_set.issubset( user_roles_set ): + accessible = True + break + else: + accessible = True + if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions + # TODO: keep access permissions as they originally were, rather than automatically making public + permissions[ trans.app.security_agent.get_action( v.action ) ] = [] + else: + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + for ldda in lddas: + # Set the DATASET permissions on the Dataset + trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) + ldda.dataset.refresh() + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + for ldda in lddas: + # Set the LIBRARY permissions on the LibraryDataset + # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions + trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) + ldda.library_dataset.refresh() + # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation + trans.app.security_agent.set_all_library_permissions( ldda, permissions ) + ldda.refresh() + if not accessible: + msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas ) + msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, " + msg += "so access permissions were not set. All other permissions were updated for the datasets." + messagetype = 'error' + else: + msg = "Permissions have been updated on %d datasets" % len( lddas ) + return trans.fill_template( "/admin/library/ldda_permissions.mako", + lddas=lddas, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + if len( obj_ids ) > 1: + # Ensure that the permissions across all library items are identical, otherwise we can't update them together. + check_list = [] + for ldda in lddas: + permissions = [] + # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation + # will always be the same as the permissions on the associated LibraryDataset, so we only need to + # check one Library object + for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): + if library_permission.action not in permissions: + permissions.append( library_permission.action ) + for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): + if dataset_permission.action not in permissions: + permissions.append( dataset_permission.action ) + permissions.sort() + if not check_list: + check_list = permissions + if permissions != check_list: + msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + return trans.fill_template( "/admin/library/ldda_permissions.mako", + lddas=lddas, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def upload_library_dataset( self, trans, library_id, folder_id, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) deleted = util.string_as_bool( params.get( 'deleted', False ) ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) - dbkey = params.get( 'dbkey', None ) + dbkey = params.get( 'dbkey', '?' ) if isinstance( dbkey, list ): last_used_build = dbkey[0] else: @@ -427,10 +675,6 @@ last_used_build = replace_dataset.library_dataset_dataset_association.dbkey else: replace_dataset = None - # Let's not overwrite the imported datatypes module with the variable datatypes? - # The built-in 'id' is overwritten in lots of places as well - ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] - ldatatypes.sort() if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ): # See if we have any inherited templates, but do not inherit contents. info_association, inherited = folder.get_info_association( inherited=True ) @@ -441,7 +685,7 @@ template_id = 'None' widgets = [] upload_option = params.get( 'upload_option', 'upload_file' ) - created_outputs = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans, + created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, controller='library_admin', library_id=library_id, folder_id=folder_id, @@ -466,345 +710,44 @@ messagetype='error' trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, created_ldda_ids=",".join( [ str( v.id ) for v in created_outputs.values() ] ), msg=util.sanitize_text( msg ), messagetype=messagetype ) ) - elif not id or replace_dataset: - # See if we have any inherited templates, but do not inherit contents. - widgets = folder.get_template_widgets( trans, get_contents=False ) - upload_option = params.get( 'upload_option', 'upload_file' ) - # No dataset(s) specified, so display the upload form. Send list of data formats to the form - # so the "extension" select list can be populated dynamically - file_formats = trans.app.datatypes_registry.upload_file_formats - # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically - def get_dbkey_options( last_used_build ): - for dbkey, build_name in util.dbnames: - yield build_name, dbkey, ( dbkey==last_used_build ) - dbkeys = get_dbkey_options( last_used_build ) - # Send list of roles to the form so the dataset can be associated with 1 or more of them. - roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() - # Send the current history to the form to enable importing datasets from history to library - history = trans.get_history() - history.refresh() - # If we're using nginx upload, override the form action - action = web.url_for( controller='library_admin', action='library_dataset_dataset_association' ) - if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: - action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action - return trans.fill_template( '/admin/library/upload.mako', - upload_option=upload_option, - action=action, - library_id=library_id, - folder_id=folder_id, - replace_dataset=replace_dataset, - file_formats=file_formats, - dbkeys=dbkeys, - last_used_build=last_used_build, - roles=roles, - history=history, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - else: - if params.get( 'permissions', False ): - action = 'permissions' - elif params.get( 'edit_info', False ): - action = 'edit_info' - else: - action = 'info' - if id.count( ',' ): - ids = id.split( ',' ) - id = None - else: - ids = None - if id: - # ldda_id specified, display attributes form - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda: - msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) - return trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - # See if we have any associated templates - widgets = ldda.get_template_widgets( trans ) - if action == 'permissions': - if params.get( 'update_roles_button', False ): - permissions = {} - accessible = False - for k, v in trans.app.model.Dataset.permitted_actions.items(): - # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not - # the DATASET_ACCESS permission, making the former useless. Need to display a warning message. - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible - if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - if len( in_roles ) > 1: - # Get the set of all users that are being associated with the dataset - in_roles_set = set() - for role in in_roles: - in_roles_set.add( role ) - users_set = set() - for role in in_roles: - for ura in role.users: - users_set.add( ura.user ) - # Make sure that at least 1 user has every role being associated with the dataset - for user in users_set: - user_roles_set = set() - for ura in user.roles: - user_roles_set.add( ura.role ) - if in_roles_set.issubset( user_roles_set ): - accessible = True - break - else: - accessible = True - if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions - # TODO: keep access permissions as they originally were, rather than automatically making public - permissions[ trans.app.security_agent.get_action( v.action ) ] = [] - else: - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - # Set the DATASET permissions on the Dataset - trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) - ldda.dataset.refresh() - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) - ldda.library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( ldda, permissions ) - ldda.refresh() - if not accessible: - msg = "At least 1 user must have every role associated with accessing dataset '%s'. " % ldda.name - msg += "The roles you attempted to associate for access would make this dataset inaccessible by everyone, " - msg += "so access permissions were not set. All other permissions were updated for the dataset." - messagetype = 'error' - else: - msg = "Permissions updated for dataset '%s'" % ldda.name - return trans.fill_template( '/admin/library/ldda_permissions.mako', - ldda=ldda, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - elif action == 'info': - return trans.fill_template( '/admin/library/ldda_info.mako', - ldda=ldda, - library_id=library_id, - deleted=deleted, - show_deleted=show_deleted, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif action == 'edit_info': - if params.get( 'change', False ): - # The user clicked the Save button on the 'Change data type' form - if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: - trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() - msg = "Data type changed for library dataset '%s'" % ldda.name - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - else: - return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) ) - elif params.get( 'save', False ): - # The user clicked the Save button on the 'Edit Attributes' form - old_name = ldda.name - new_name = util.restore_text( params.get( 'name', '' ) ) - new_info = util.restore_text( params.get( 'info', '' ) ) - new_message = util.restore_text( params.get( 'message', '' ) ) - if not new_name: - msg = 'Enter a valid name' - messagetype = 'error' - else: - ldda.name = new_name - ldda.info = new_info - ldda.message = new_message - # The following for loop will save all metadata_spec items - for name, spec in ldda.datatype.metadata_spec.items(): - if spec.get("readonly"): - continue - optional = params.get( "is_" + name, None ) - if optional and optional == 'true': - # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( ldda.metadata, name, None ) - else: - setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) - ldda.metadata.dbkey = dbkey - ldda.datatype.after_edit( ldda ) - trans.app.model.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif params.get( 'detect', False ): - # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in ldda.datatype.metadata_spec.items(): - # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: - if spec.get( 'default' ): - setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - ldda.datatype.set_meta( ldda ) - ldda.datatype.after_edit( ldda ) - trans.app.model.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif params.get( 'delete', False ): - ldda.deleted = True - ldda.flush() - msg = 'Dataset %s has been removed from this library' % ldda.name - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - ldda.datatype.before_edit( ldda ) - if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: - # Copy dbkey into metadata, for backwards compatability - # This looks like it does nothing, but getting the dbkey - # returns the metadata dbkey unless it is None, in which - # case it resorts to the old dbkey. Setting the dbkey - # sets it properly in the metadata - ldda.metadata.dbkey = ldda.dbkey - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif ids: - # Multiple ids specfied, display permission form, permissions will be updated for all simultaneously. - lddas = [] - for id in [ int( id ) for id in ids ]: - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if ldda is None: - msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) - trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - lddas.append( ldda ) - if len( lddas ) < 2: - msg = 'You must specify at least two datasets on which to modify permissions, ids you sent: %s' % str( ids ) - trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - if action == 'permissions': - if params.get( 'update_roles_button', False ): - permissions = {} - accessible = False - for k, v in trans.app.model.Dataset.permitted_actions.items(): - # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not - # the DATASET_ACCESS permission, making the former useless. Need to display a warning message. - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible - if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - if len( in_roles ) > 1: - # Get the set of all users that are being associated with the dataset - in_roles_set = set() - for role in in_roles: - in_roles_set.add( role ) - users_set = set() - for role in in_roles: - for ura in role.users: - users_set.add( ura.user ) - # Make sure that at least 1 user has every role being associated with the dataset - for user in users_set: - user_roles_set = set() - for ura in user.roles: - user_roles_set.add( ura.role ) - if in_roles_set.issubset( user_roles_set ): - accessible = True - break - else: - accessible = True - if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions - # TODO: keep access permissions as they originally were, rather than automatically making public - permissions[ trans.app.security_agent.get_action( v.action ) ] = [] - else: - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the DATASET permissions on the Dataset - trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) - ldda.dataset.refresh() - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) - ldda.library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( ldda, permissions ) - ldda.refresh() - if not accessible: - msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas ) - msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, " - msg += "so access permissions were not set. All other permissions were updated for the datasets." - messagetype = 'error' - else: - msg = "Permissions have been updated on %d datasets" % len( lddas ) - return trans.fill_template( "/admin/library/ldda_permissions.mako", - ldda=lddas, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - # Ensure that the permissions across all library items are identical, otherwise we can't update them together. - check_list = [] - for ldda in lddas: - permissions = [] - # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation - # will always be the same as the permissions on the associated LibraryDataset, so we only need to - # check one Library object - for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): - if library_permission.action not in permissions: - permissions.append( library_permission.action ) - for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): - if dataset_permission.action not in permissions: - permissions.append( dataset_permission.action ) - permissions.sort() - if not check_list: - check_list = permissions - if permissions != check_list: - msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' - trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - return trans.fill_template( "/admin/library/ldda_permissions.mako", - ldda=lddas, - library_id=library_id, - msg=msg, - messagetype=messagetype ) + # See if we have any inherited templates, but do not inherit contents. + widgets = folder.get_template_widgets( trans, get_contents=False ) + upload_option = params.get( 'upload_option', 'upload_file' ) + # No dataset(s) specified, so display the upload form. Send list of data formats to the form + # so the "extension" select list can be populated dynamically + file_formats = trans.app.datatypes_registry.upload_file_formats + # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically + def get_dbkey_options( last_used_build ): + for dbkey, build_name in util.dbnames: + yield build_name, dbkey, ( dbkey==last_used_build ) + dbkeys = get_dbkey_options( last_used_build ) + # Send list of roles to the form so the dataset can be associated with 1 or more of them. + roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() + # Send the current history to the form to enable importing datasets from history to library + history = trans.get_history() + history.refresh() + # If we're using nginx upload, override the form action + action = web.url_for( controller='library_admin', action='upload_library_dataset' ) + if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: + action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action + return trans.fill_template( '/admin/library/upload.mako', + upload_option=upload_option, + action=action, + library_id=library_id, + folder_id=folder_id, + replace_dataset=replace_dataset, + file_formats=file_formats, + dbkeys=dbkeys, + last_used_build=last_used_build, + roles=roles, + history=history, + widgets=widgets, + msg=msg, + messagetype=messagetype ) @web.expose @web.require_admin def add_history_datasets_to_library( self, trans, library_id, folder_id, hda_ids='', **kwd ): @@ -817,7 +760,7 @@ msg = "Invalid folder id: %s" % str( folder_id ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) replace_id = params.get( 'replace_id', None ) @@ -832,7 +775,7 @@ msg = 'Your current history is empty' return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) if params.get( 'add_history_datasets_to_library_button', False ): @@ -857,7 +800,7 @@ msg = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) if created_ldda_ids: @@ -875,7 +818,7 @@ msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, created_ldda_ids=created_ldda_ids, msg=util.sanitize_text( msg ), messagetype='done' ) ) @@ -908,146 +851,15 @@ messagetype=messagetype ) @web.expose @web.require_admin - def info_template( self, trans, library_id, id=None, folder_id=None, ldda_id=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if id: - library_item = trans.app.model.FormDefinition.get( int( id ) ) - library_item_desc = 'information template' - response_action = 'info_template' - response_id = id - elif folder_id: - library_item = trans.app.model.LibraryFolder.get( int( folder_id ) ) - library_item_desc = 'folder' - response_action = 'folder' - response_id = folder_id - elif ldda_id: - library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_id ) ) - library_item_desc = 'library dataset' - response_action = 'library_dataset_dataset_association' - response_id = ldda_id - else: - library_item = trans.app.model.Library.get( int( library_id ) ) - library_item_desc = 'library' - response_action = 'browse_library' - response_id = library_id - forms = get_all_forms( trans, - filter=dict( deleted=False ), - form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) - if not forms: - msg = "There are no forms on which to base the template, so create a form and " - msg += "try again to add the information template to the %s." % library_item_desc - trans.response.send_redirect( web.url_for( controller='forms', - action='new', - new=True, - msg=msg, - messagetype='done' ) ) - if params.get( 'add', False ): - if params.get( 'add_info_template_button', False ): - form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) ) - #fields = list( copy.deepcopy( form.fields ) ) - form_values = trans.app.model.FormValues( form, [] ) - form_values.flush() - if folder_id: - assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values ) - elif ldda_id: - assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values ) - else: - assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values ) - assoc.flush() - msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) - trans.response.send_redirect( web.url_for( controller='library_admin', - action=response_action, - id=response_id, - msg=msg, - message_type='done' ) ) - return trans.fill_template( '/admin/library/select_info_template.mako', - library_item_name=library_item.name, - library_item_desc=library_item_desc, - library_id=library_id, - folder_id=folder_id, - ldda_id=ldda_id, - forms=forms, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def edit_template_info( self, trans, library_id, num_widgets, library_item_id=None, library_item_type=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - folder_id = None - if library_item_type == 'library': - library_item = trans.app.model.Library.get( library_item_id ) - elif library_item_type == 'library_dataset': - library_item = trans.app.model.LibraryDataset.get( library_item_id ) - elif library_item_type == 'folder': - library_item = trans.app.model.LibraryFolder.get( library_item_id ) - elif library_item_type == 'library_dataset_dataset_association': - library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id ) - # This response_action method requires a folder_id - folder_id = library_item.library_dataset.folder.id - else: - msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) ) + def download_dataset_from_folder(self, trans, obj_id, library_id=None, **kwd): + """Catches the dataset id and displays file contents as directed""" + # id must refer to a LibraryDatasetDatasetAssociation object + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if not ldda.dataset: + msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - # Save updated template field contents - field_contents = [] - for index in range( int( num_widgets ) ): - field_contents.append( util.restore_text( params.get( 'field_%i' % ( index ), '' ) ) ) - if field_contents: - # Since information templates are inherited, the template fields can be displayed on the information - # page for a folder or library dataset when it has no info_association object. If the user has added - # field contents on an inherited template via a parent's info_association, we'll need to create a new - # form_values and info_association for the current object. The value for the returned inherited variable - # is not applicable at this level. - info_association, inherited = library_item.get_info_association( restrict=True ) - if info_association: - template = info_association.template - info = info_association.info - form_values = trans.app.model.FormValues.get( info.id ) - # Update existing content only if it has changed - if form_values.content != field_contents: - form_values.content = field_contents - form_values.flush() - else: - # Inherit the next available info_association so we can get the template - info_association, inherited = library_item.get_info_association() - template = info_association.template - # Create a new FormValues object - form_values = trans.app.model.FormValues( template, field_contents ) - form_values.flush() - # Create a new info_association between the current library item and form_values - if library_item_type == 'folder': - info_association = trans.app.model.LibraryFolderInfoAssociation( library_item, template, form_values ) - info_association.flush() - elif library_item_type == 'library_dataset_dataset_association': - info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, template, form_values ) - info_association.flush() - msg = 'The information has been updated.' - return trans.response.send_redirect( web.url_for( controller='library_admin', - action=library_item_type, - id=library_item.id, - library_id=library_id, - folder_id=folder_id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - @web.expose - @web.require_admin - def download_dataset_from_folder(self, trans, id, library_id=None, **kwd): - """Catches the dataset id and displays file contents as directed""" - # id must refer to a LibraryDatasetDatasetAssociation object - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( id ) - return trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) @@ -1057,14 +869,14 @@ valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = ldda.name fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( id ), fname ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname ) try: return open( ldda.file_name ) except: msg = 'This dataset contains no content' return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) @web.expose @@ -1076,48 +888,40 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) if params.get( 'action_on_datasets_button', False ): - if not params.ldda_ids: + ldda_ids = util.listify( params.get( 'ldda_ids', None ) ) + if not ldda_ids: msg = "At least one dataset must be selected for %s" % params.action trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) - ldda_ids = util.listify( params.ldda_ids ) - if params.action == 'edit': + if params.action == 'manage_permissions': # We need the folder containing the LibraryDatasetDatasetAssociation(s) - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_ids[0] ) + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_ids[0] ) ) trans.response.send_redirect( web.url_for( controller='library_admin', - action='library_dataset_dataset_association', + action='ldda_manage_permissions', library_id=library_id, folder_id=ldda.library_dataset.folder.id, - id=",".join( ldda_ids ), - permissions=True, + obj_id=",".join( ldda_ids ), msg=util.sanitize_text( msg ), messagetype=messagetype ) ) elif params.action == 'delete': - for id in ldda_ids: - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) + for ldda_id in ldda_ids: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) ldda.deleted = True ldda.flush() - msg = "The selected datasets have been removed from this library" + msg = "The selected datasets have been removed from this data library" trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, show_deleted=False, msg=util.sanitize_text( msg ), messagetype='done' ) ) - else: - msg = "Action %s is not yet implemented" % str( params.action ) - trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) else: trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', - id=library_id, + obj_id=library_id, msg=util.sanitize_text( msg ), messagetype=messagetype ) ) @web.expose @@ -1149,7 +953,10 @@ if library_item_type == 'library': return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) else: - return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) + return self.browse_library( trans, + obj_id=library_id, + msg=msg, + messagetype=messagetype ) @web.expose @web.require_admin def undelete_library_item( self, trans, library_id, library_item_id, library_item_type ): @@ -1177,4 +984,7 @@ if library_item_type == 'library': return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) else: - return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) + return self.browse_library( trans, + obj_id=library_id, + msg=msg, + messagetype=messagetype ) diff -r 6a066b05c94f -r 22addc979108 lib/galaxy/web/controllers/library_common.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/controllers/library_common.py Wed Sep 30 05:16:17 2009 -0400 @@ -0,0 +1,300 @@ +import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile +from galaxy.web.base.controller import * +from galaxy import util, jobs +from galaxy.datatypes import sniff +from galaxy.security import RBACAgent +from galaxy.util.json import to_json_string +from galaxy.tools.actions import upload_common +from galaxy.web.controllers.forms import get_all_forms +from galaxy.model.orm import * + +log = logging.getLogger( __name__ ) + +class LibraryCommon( BaseController ): + @web.json + def library_item_updates( self, trans, ids=None, states=None ): + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + # Create new HTML for any that have changed + rval = {} + if ids is not None and states is not None: + ids = map( int, ids.split( "," ) ) + states = states.split( "," ) + for id, state in zip( ids, states ): + data = self.app.model.LibraryDatasetDatasetAssociation.get( id ) + if data.state != state: + job_ldda = data + while job_ldda.copied_from_library_dataset_dataset_association: + job_ldda = job_ldda.copied_from_library_dataset_dataset_association + force_history_refresh = False + rval[id] = { + "state": data.state, + "html": unicode( trans.fill_template( "library/library_item_info.mako", ldda=data ), 'utf-8' ) + #"force_history_refresh": force_history_refresh + } + return rval + def upload_dataset( self, trans, controller, library_id, folder_id, replace_dataset=None, **kwd ): + # Set up the traditional tool state/params + tool_id = 'upload1' + tool = trans.app.toolbox.tools_by_id[ tool_id ] + state = tool.new_state( trans ) + errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd, changed_dependencies={} ) + tool_params = state.inputs + dataset_upload_inputs = [] + for input_name, input in tool.inputs.iteritems(): + if input.type == "upload_dataset": + dataset_upload_inputs.append( input ) + # Library-specific params + params = util.Params( kwd ) # is this filetoolparam safe? + library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + server_dir = util.restore_text( params.get( 'server_dir', '' ) ) + if replace_dataset not in [ None, 'None' ]: + replace_id = replace_dataset.id + else: + replace_id = None + upload_option = params.get( 'upload_option', 'upload_file' ) + err_redirect = False + if upload_option == 'upload_directory': + if server_dir in [ None, 'None', '' ]: + err_redirect = True + if controller == 'library_admin': + import_dir = trans.app.config.library_import_dir + import_dir_desc = 'library_import_dir' + full_dir = os.path.join( import_dir, server_dir ) + else: + import_dir = trans.app.config.user_library_import_dir + import_dir_desc = 'user_library_import_dir' + if server_dir == trans.user.email: + full_dir = os.path.join( import_dir, server_dir ) + else: + full_dir = os.path.join( import_dir, trans.user.email, server_dir ) + if import_dir: + msg = 'Select a directory' + else: + msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc + # Proceed with (mostly) regular upload processing + precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=controller ) + if upload_option == 'upload_file': + tool_params = upload_common.persist_uploads( tool_params ) + uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) + elif upload_option == 'upload_directory': + uploaded_datasets = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) + upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) + if upload_option == 'upload_file' and not uploaded_datasets: + msg = 'Select a file, enter a URL or enter text' + err_redirect = True + if err_redirect: + trans.response.send_redirect( web.url_for( controller=controller, + action='upload_library_dataset', + library_id=library_id, + folder_id=folder_id, + replace_id=replace_id, + upload_option=upload_option, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + json_file_path = upload_common.create_paramfile( uploaded_datasets ) + data_list = [ ud.data for ud in uploaded_datasets ] + return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) + def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): + files = [] + try: + for entry in os.listdir( full_dir ): + # Only import regular files + if os.path.isfile( os.path.join( full_dir, entry ) ): + files.append( entry ) + except Exception, e: + msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) + err_redirect = True + return None + if not files: + msg = "The directory '%s' contains no valid files" % full_dir + err_redirect = True + return None + uploaded_datasets = [] + for file in files: + library_bunch.replace_dataset = None + uploaded_dataset = util.bunch.Bunch() + uploaded_dataset.path = os.path.join( full_dir, file ) + if not os.path.isfile( uploaded_dataset.path ): + continue + uploaded_dataset.type = 'server_dir' + uploaded_dataset.name = file + uploaded_dataset.ext = None + uploaded_dataset.file_type = params.file_type + uploaded_dataset.dbkey = params.dbkey + uploaded_dataset.space_to_tab = params.space_to_tab + uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch ) + uploaded_datasets.append( uploaded_dataset ) + return uploaded_datasets + @web.expose + def info_template( self, trans, cntrller, library_id, response_action='library', obj_id=None, folder_id=None, ldda_id=None, **kwd ): + # Only adding a new templAte to a library or folder is currently allowed. Editing an existing template is + # a future enhancement. The response_action param is the name of the method to which this method will redirect + # if a new template is being added to a library or folder. + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if obj_id: + library_item = trans.app.model.FormDefinition.get( int( obj_id ) ) + library_item_desc = 'information template' + response_id = obj_id + elif folder_id: + library_item = trans.app.model.LibraryFolder.get( int( folder_id ) ) + library_item_desc = 'folder' + response_id = folder_id + elif ldda_id: + library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_id ) ) + library_item_desc = 'library dataset' + response_id = ldda_id + else: + library_item = trans.app.model.Library.get( int( library_id ) ) + library_item_desc = 'library' + response_id = library_id + forms = get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) + if not forms: + msg = "There are no forms on which to base the template, so create a form and " + msg += "try again to add the information template to the %s." % library_item_desc + trans.response.send_redirect( web.url_for( controller='forms', + action='new', + new=True, + msg=msg, + messagetype='done' ) ) + if params.get( 'add_info_template_button', False ): + form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) ) + #fields = list( copy.deepcopy( form.fields ) ) + form_values = trans.app.model.FormValues( form, [] ) + form_values.flush() + if folder_id: + assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values ) + elif ldda_id: + assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values ) + else: + assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values ) + assoc.flush() + msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) + trans.response.send_redirect( web.url_for( controller=cntrller, + action=response_action, + obj_id=response_id, + msg=msg, + message_type='done' ) ) + # TODO: handle this better + if cntrller == 'library_admin': + tmplt = '/admin/library/select_info_template.mako' + else: + tmplt = '/ibrary/select_info_template.mako' + return trans.fill_template( tmplt, + library_item_name=library_item.name, + library_item_desc=library_item_desc, + library_id=library_id, + folder_id=folder_id, + ldda_id=ldda_id, + forms=forms, + msg=msg, + messagetype=messagetype ) + @web.expose + def edit_template_info( self, trans, cntrller, library_id, response_action, num_widgets, library_item_id=None, library_item_type=None, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + folder_id = None + if library_item_type == 'library': + library_item = trans.app.model.Library.get( library_item_id ) + elif library_item_type == 'library_dataset': + library_item = trans.app.model.LibraryDataset.get( library_item_id ) + elif library_item_type == 'folder': + library_item = trans.app.model.LibraryFolder.get( library_item_id ) + elif library_item_type == 'library_dataset_dataset_association': + library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id ) + # This response_action method requires a folder_id + folder_id = library_item.library_dataset.folder.id + else: + msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) ) + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + # Save updated template field contents + field_contents = [] + for index in range( int( num_widgets ) ): + field_contents.append( util.restore_text( params.get( 'field_%i' % ( index ), '' ) ) ) + if field_contents: + # Since information templates are inherited, the template fields can be displayed on the information + # page for a folder or library dataset when it has no info_association object. If the user has added + # field contents on an inherited template via a parent's info_association, we'll need to create a new + # form_values and info_association for the current object. The value for the returned inherited variable + # is not applicable at this level. + info_association, inherited = library_item.get_info_association( restrict=True ) + if info_association: + template = info_association.template + info = info_association.info + form_values = trans.app.model.FormValues.get( info.id ) + # Update existing content only if it has changed + if form_values.content != field_contents: + form_values.content = field_contents + form_values.flush() + else: + # Inherit the next available info_association so we can get the template + info_association, inherited = library_item.get_info_association() + template = info_association.template + # Create a new FormValues object + form_values = trans.app.model.FormValues( template, field_contents ) + form_values.flush() + # Create a new info_association between the current library item and form_values + if library_item_type == 'folder': + info_association = trans.app.model.LibraryFolderInfoAssociation( library_item, template, form_values ) + info_association.flush() + elif library_item_type == 'library_dataset_dataset_association': + info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, template, form_values ) + info_association.flush() + msg = 'The information has been updated.' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action=response_action, + library_id=library_id, + folder_id=folder_id, + obj_id=library_item.id, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + +# ---- Utility methods ------------------------------------------------------- + +def active_folders( trans, folder ): + # Much faster way of retrieving all active sub-folders within a given folder than the + # performance of the mapper. This query also eagerloads the permissions on each folder. + return trans.sa_session.query( trans.app.model.LibraryFolder ) \ + .filter_by( parent=folder, deleted=False ) \ + .options( eagerload_all( "actions" ) ) \ + .order_by( trans.app.model.LibraryFolder.table.c.name ) \ + .all() +def activatable_folders( trans, folder ): + return trans.sa_session.query( trans.app.model.LibraryFolder ) \ + .filter_by( parent=folder, purged=False ) \ + .options( eagerload_all( "actions" ) ) \ + .order_by( trans.app.model.LibraryFolder.table.c.name ) \ + .all() +def active_folders_and_lddas( trans, folder ): + folders = active_folders( trans, folder ) + # This query is much faster than the folder.active_library_datasets property + lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \ + .filter_by( deleted=False ) \ + .join( "library_dataset" ) \ + .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \ + .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \ + .all() + return folders, lddas +def activatable_folders_and_lddas( trans, folder ): + folders = activatable_folders( trans, folder ) + # This query is much faster than the folder.activatable_library_datasets property + lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \ + .join( "library_dataset" ) \ + .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \ + .join( "dataset" ) \ + .filter( trans.app.model.Dataset.table.c.deleted==False ) \ + .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \ + .all() + return folders, lddas diff -r 6a066b05c94f -r 22addc979108 lib/galaxy/web/controllers/library_dataset.py --- a/lib/galaxy/web/controllers/library_dataset.py Tue Sep 29 21:51:51 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile -from galaxy.web.base.controller import * -from galaxy import util, jobs -from galaxy.datatypes import sniff -from galaxy.security import RBACAgent -from galaxy.util.json import to_json_string -from galaxy.tools.actions import upload_common - -log = logging.getLogger( __name__ ) - -class UploadLibraryDataset( BaseController ): - @web.json - def library_item_updates( self, trans, ids=None, states=None ): - # Avoid caching - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - # Create new HTML for any that have changed - rval = {} - if ids is not None and states is not None: - ids = map( int, ids.split( "," ) ) - states = states.split( "," ) - for id, state in zip( ids, states ): - data = self.app.model.LibraryDatasetDatasetAssociation.get( id ) - if data.state != state: - job_ldda = data - while job_ldda.copied_from_library_dataset_dataset_association: - job_ldda = job_ldda.copied_from_library_dataset_dataset_association - force_history_refresh = False - rval[id] = { - "state": data.state, - "html": unicode( trans.fill_template( "library/library_item_info.mako", ldda=data ), 'utf-8' ) - #"force_history_refresh": force_history_refresh - } - return rval - def upload_dataset( self, trans, controller, library_id, folder_id, replace_dataset=None, **kwd ): - # Set up the traditional tool state/params - tool_id = 'upload1' - tool = trans.app.toolbox.tools_by_id[ tool_id ] - state = tool.new_state( trans ) - errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd, changed_dependencies={} ) - tool_params = state.inputs - dataset_upload_inputs = [] - for input_name, input in tool.inputs.iteritems(): - if input.type == "upload_dataset": - dataset_upload_inputs.append( input ) - # Library-specific params - params = util.Params( kwd ) # is this filetoolparam safe? - library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - server_dir = util.restore_text( params.get( 'server_dir', '' ) ) - if replace_dataset not in [ None, 'None' ]: - replace_id = replace_dataset.id - else: - replace_id = None - upload_option = params.get( 'upload_option', 'upload_file' ) - err_redirect = False - if upload_option == 'upload_directory': - if server_dir in [ None, 'None', '' ]: - err_redirect = True - if controller == 'library_admin': - import_dir = trans.app.config.library_import_dir - import_dir_desc = 'library_import_dir' - full_dir = os.path.join( import_dir, server_dir ) - else: - import_dir = trans.app.config.user_library_import_dir - import_dir_desc = 'user_library_import_dir' - if server_dir == trans.user.email: - full_dir = os.path.join( import_dir, server_dir ) - else: - full_dir = os.path.join( import_dir, trans.user.email, server_dir ) - if import_dir: - msg = 'Select a directory' - else: - msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc - # Proceed with (mostly) regular upload processing - precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=controller ) - if upload_option == 'upload_file': - tool_params = upload_common.persist_uploads( tool_params ) - uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) - elif upload_option == 'upload_directory': - uploaded_datasets = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) - upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) - if upload_option == 'upload_file' and not uploaded_datasets: - msg = 'Select a file, enter a URL or enter text' - err_redirect = True - if err_redirect: - trans.response.send_redirect( web.url_for( controller=controller, - action='library_dataset_dataset_association', - library_id=library_id, - folder_id=folder_id, - replace_id=replace_id, - upload_option=upload_option, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - json_file_path = upload_common.create_paramfile( uploaded_datasets ) - data_list = [ ud.data for ud in uploaded_datasets ] - return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) - def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): - files = [] - try: - for entry in os.listdir( full_dir ): - # Only import regular files - if os.path.isfile( os.path.join( full_dir, entry ) ): - files.append( entry ) - except Exception, e: - msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) - err_redirect = True

1 0

[hg] galaxy 2797: Added grid to view/filter datasets. To view da...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e7b9d15e8e93 changeset: 2797:e7b9d15e8e93 user: jeremy goecks <jeremy.goecks at emory.edu> date: Tue Sep 29 17:57:45 2009 -0400 description: Added grid to view/filter datasets. To view datasets grid: User (tab)-->My Data-->Datasets 7 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py lib/galaxy/web/framework/helpers/grids.py templates/base_panels.mako templates/dataset/grid.mako templates/history/grid.mako templates/my_data.mako diffs (590 lines): diff -r b819249af24d -r e7b9d15e8e93 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Sep 29 17:14:20 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue Sep 29 17:57:45 2009 -0400 @@ -1,6 +1,8 @@ import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib from galaxy.web.base.controller import * +from galaxy.tags.tag_handler import TagHandler +from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy import util, datatypes, jobs, web, model from cgi import escape, FieldStorage @@ -42,7 +44,97 @@ (This is an automated message). """ +class HistoryDatasetAssociationListGrid( grids.Grid ): + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, hda ): + if hda.deleted: + return "deleted" + return "" + def get_link( self, trans, grid, hda ): + return None + class TagsColumn( grids.GridColumn ): + def __init__(self, col_name, key, filterable): + grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) + # Tags cannot be sorted. + self.sortable = False + self.tag_elt_id_gen = 0 + def get_value( self, trans, grid, hda ): + self.tag_elt_id_gen += 1 + elt_id="tagging-elt" + str( self.tag_elt_id_gen ) + div_elt = "<div id=%s></div>" % elt_id + return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=hda, + elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) + def filter( self, db_session, query, column_filter ): + """ Modify query to include only hdas with tags in column_filter. """ + if column_filter == "All": + pass + elif column_filter: + # Parse filter to extract multiple tags. + tag_handler = TagHandler() + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + for name, value in raw_tags.items(): + tag = tag_handler.get_tag_by_name( db_session, name ) + if tag: + query = query.filter( model.HistoryDatasetAssociation.tags.any( tag_id=tag.id ) ) + if value: + query = query.filter( model.HistoryDatasetAssociation.tags.any( value=value.lower() ) ) + else: + # Tag doesn't exist; unclear what to do here, but the literal thing to do is add the criterion, which + # will then yield a query that returns no results. + query = query.filter( model.HistoryDatasetAssociation.tags.any( user_tname=name ) ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = { "All": "All" } + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, hda ): + if hda.deleted: + return "deleted" + return "" + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" } + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + + # Grid definition + title = "Stored datasets" + model_class = model.HistoryDatasetAssociation + template='/dataset/grid.mako' + default_sort_key = "-create_time" + columns = [ + grids.GridColumn( "Name", key="name", + # Link name to dataset's history. + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ) ), + TagsColumn( "Tags", key="tags", filterable=True ), + StatusColumn( "Status", key="deleted", attach_popup=False ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + ] + operations = [] + standard_filters = [] + default_filter = dict( deleted="False", tags="All" ) + preserve_state = False + use_paging = True + num_rows_per_page = 10 + def apply_default_filter( self, trans, query, **kwargs ): + # This is a somewhat obtuse way to join the History and HDA tables. However, it's necessary + # because the initial query in build_initial_query is specificied on the HDA table (this is reasonable) + # and there's no simple property in the HDA to do the join. + return query.select_from( model.HistoryDatasetAssociation.table.join( model.History.table ) ).filter( model.History.user == trans.user ) + class DatasetInterface( BaseController ): + + stored_list_grid = HistoryDatasetAssociationListGrid() @web.expose def errors( self, trans, id ): @@ -136,7 +228,50 @@ raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % ( filename ) ) else: return trans.show_error_message( "You are not allowed to access this dataset" ) - + + @web.expose + @web.require_login( "see all available datasets" ) + def list( self, trans, **kwargs ): + """List all available datasets""" + status = message = None + + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + hda_ids = util.listify( kwargs.get( 'id', [] ) ) + + # Display no message by default + status, message = None, None + + # Load the hdas and ensure they all belong to the current user + hdas = [] + for encoded_hda_id in hda_ids: + hda_id = trans.security.decode_id( encoded_hda_id ) + hda = trans.sa_session.query( model.HistoryDatasetAssociation ).filter_by( id=hda_id ).first() + if hda: + # Ensure history is owned by current user + if hda.history.user_id != None and trans.user: + assert trans.user.id == hda.history.user_id, "HistoryDatasetAssocation does not belong to current user" + hdas.append( hda ) + else: + log.warn( "Invalid history_dataset_association id '%r' passed to list", hda_id ) + + if hdas: + + if operation == "switch": + # Convert hda to histories. + histories = [] + for hda in hdas: + histories.append( hda.history ) + + # Use history controller to switch the history. TODO: is this reasonable? + status, message = trans.webapp.controllers['history']._list_switch( trans, histories ) + + # Current history changed, refresh history frame + trans.template_context['refresh_frames'] = ['history'] + + # Render the list view + return self.stored_list_grid( trans, status=status, message=message, **kwargs ) + @web.expose def display_at( self, trans, dataset_id, filename=None, **kwd ): """Sets up a dataset permissions so it is viewable at an external site""" @@ -222,7 +357,7 @@ new_history = trans.app.model.History() if new_history_name: new_history.name = new_history_name - new_history.user = user + new_history_name = user new_history.flush() target_history_ids.append( new_history.id ) if user: diff -r b819249af24d -r e7b9d15e8e93 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Sep 29 17:14:20 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Tue Sep 29 17:57:45 2009 -0400 @@ -46,6 +46,13 @@ yield "</body></html>" ## ---- Root history display --------------------------------------------- + + @web.expose + def my_data( self, trans ): + """ + Display user's data. + """ + return trans.fill_template_mako( "/my_data.mako" ) @web.expose def history( self, trans, as_xml=False, show_deleted=False ): diff -r b819249af24d -r e7b9d15e8e93 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Sep 29 17:14:20 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Sep 29 17:57:45 2009 -0400 @@ -70,18 +70,19 @@ use_default_filter_str = kwargs.get( 'use_default_filter' ) use_default_filter = False if use_default_filter_str: - use_default_filter = use_default_filter_str.lower() == 'true' + use_default_filter = ( use_default_filter_str.lower() == 'true' ) # Process filtering arguments to (a) build a query that represents the filter and (b) builds a # dictionary that denotes the current filter. cur_filter_dict = {} for column in self.columns: if column.key: - # Get the filter criterion for the column. Precedence is (a) if using default filter, look there; (b) look in kwargs; and (c) look in - # base filter. + # Get the filter criterion for the column. Precedence is (a) if using default filter, only look there; otherwise, + # (b) look in kwargs; and (c) look in base filter. column_filter = None - if use_default_filter and self.default_filter: - column_filter = self.default_filter.get( column.key ) + if use_default_filter: + if self.default_filter: + column_filter = self.default_filter.get( column.key ) elif "f-" + column.key in kwargs: column_filter = kwargs.get( "f-" + column.key ) elif column.key in base_filter: @@ -130,7 +131,6 @@ # be computed. total_num_rows = query.count() query = query.limit( self.num_rows_per_page ).offset( ( page_num-1 ) * self.num_rows_per_page ) - num_pages = int ( math.ceil( float( total_num_rows ) / self.num_rows_per_page ) ) else: # Defaults. diff -r b819249af24d -r e7b9d15e8e93 templates/base_panels.mako --- a/templates/base_panels.mako Tue Sep 29 17:14:20 2009 -0400 +++ b/templates/base_panels.mako Tue Sep 29 17:57:45 2009 -0400 @@ -217,6 +217,7 @@ </ul> <ul class="loggedin-only" style="${style2}"> <li>Logged in as <span id="user-email">${user_email}</span></li> + <li><a target="galaxy_main" href="${h.url_for( controller='root', action='my_data' )}">My Data</a></li> %if app.config.use_remote_user: %if app.config.remote_user_logout_href: <li><a href="${app.config.remote_user_logout_href}" target="_top">Logout</a></li> diff -r b819249af24d -r e7b9d15e8e93 templates/dataset/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/dataset/grid.mako Tue Sep 29 17:57:45 2009 -0400 @@ -0,0 +1,322 @@ +<%! from galaxy.web.framework.helpers.grids import GridColumnFilter %> + +<%inherit file="/base.mako"/> +<%def name="title()">${grid.title}</%def> + +%if message: + <p> + <div class="${message_type}message transient-message">${message}</div> + <div style="clear: both"></div> + </p> +%endif + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("jquery.autocomplete", "autocomplete_tagging" )} + <script type="text/javascript"> + ## TODO: generalize and move into galaxy.base.js + $(document).ready(function() { + $(".grid").each( function() { + var grid = this; + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var update = $(this).find( "span.grid-selected-count" ); + $(checkboxes).each( function() { + $(this).change( function() { + var n = $(checkboxes).filter("[checked]").size(); + update.text( n ); + }); + }) + }); + + // Set up autocomplete for tag filter input. + var t = $("#input-tag-filter"); + t.keyup( function( e ) + { + if ( e.keyCode == 27 ) + { + // Escape key + $(this).trigger( "blur" ); + } else if ( + ( e.keyCode == 13 ) || // Return Key + ( e.keyCode == 188 ) || // Comma + ( e.keyCode == 32 ) // Space + ) + { + // + // Check input. + // + + new_value = this.value; + + // Do nothing if return key was used to autocomplete. + if (return_key_pressed_for_autocomplete == true) + { + return_key_pressed_for_autocomplete = false; + return false; + } + + // Suppress space after a ":" + if ( new_value.indexOf(": ", new_value.length - 2) != -1) + { + this.value = new_value.substring(0, new_value.length-1); + return false; + } + + // Remove trigger keys from input. + if ( (e.keyCode == 188) || (e.keyCode == 32) ) + new_value = new_value.substring( 0 , new_value.length - 1 ); + + // Trim whitespace. + new_value = new_value.replace(/^\s+|\s+$/g,""); + + // Too short? + if (new_value.length < 3) + return false; + + // + // New tag OK. + // + } + }); + + // Add autocomplete to input. + var format_item_func = function(key, row_position, num_rows, value, search_term) + { + tag_name_and_value = value.split(":"); + return (tag_name_and_value.length == 1 ? tag_name_and_value[0] :tag_name_and_value[1]); + //var array = new Array(key, value, row_position, num_rows, + //search_term ); return "\"" + array.join("*") + "\""; + } + var autocomplete_options = + { selectFirst: false, formatItem : format_item_func, autoFill: false, highlight: false, mustMatch: true }; + + t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='HistoryDatasetAssociation' )}", autocomplete_options); + + //t.addClass("tag-input"); + + return t; + }); + ## Can this be moved into base.mako? + %if refresh_frames: + %if 'masthead' in refresh_frames: + ## Refresh masthead == user changes (backward compatibility) + if ( parent.user_changed ) { + %if trans.user: + parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); + %else: + parent.user_changed( null, false ); + %endif + } + %endif + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + %if 'tools' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_tools ) { + parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + if ( parent.force_left_panel ) { + parent.force_left_panel( 'show' ); + } + } + %endif + %endif + + // + // Add a tag to the current grid filter; this adds the tag to the filter and then issues a request to refresh the grid. + // + function add_tag_to_grid_filter(tag_name, tag_value) + { + // Use tag as a filter: replace TAGNAME with tag_name and issue query. + <% + url_args = {} + if "tags" in cur_filter_dict and cur_filter_dict["tags"] != "All": + url_args["f-tags"] = cur_filter_dict["tags"].encode("utf-8") + ", TAGNAME" + else: + url_args["f-tags"] = "TAGNAME" + %> + var url_base = "${url( url_args )}"; + var url = url_base.replace("TAGNAME", tag_name); + self.location = url; + } + + </script> +</%def> + +<%def name="stylesheets()"> + ${h.css( "base", "autocomplete_tagging" )} + <style> + ## Not generic to all grids -- move to base? + .count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; + } + </style> +</%def> + +<div class="grid-header"> + <h2>${grid.title}</h2> + + ## Print grid filter. + <form name="dataset_actions" action="javascript:add_tag_to_grid_filter($('#input-tag-filter').attr('value'))" method="get" > + <strong>Filter:   </strong> + %for column in grid.columns: + %if column.filterable: + <span> by ${column.label.lower()}:</span> + ## For now, include special case to handle tags. + %if column.key == "tags": + %if cur_filter_dict[column.key] != "All": + <span class="filter" "style='font-style: italic'"> + ${cur_filter_dict[column.key]} + </span> + <span>|</span> + %endif + <input id="input-tag-filter" name="f-tags" type="text" value="" size="15"/> + <span>|</span> + %endif + + ## Handle other columns. + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" "style='font-style: italic'">${filter.label}</span> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endif + %endfor + <span>     </span> + %endif + %endfor + </form> +</div> +<form name="dataset_actions" action="${url()}" method="post" > + <table class="grid"> + <thead> + <tr> + %for column in grid.columns: + %if column.visible: + <% + href = "" + extra = "" + if column.sortable: + if sort_key == column.key: + if sort_order == "asc": + href = url( sort=( "-" + column.key ) ) + extra = "↓" + else: + href = url( sort=( column.key ) ) + extra = "↑" + else: + href = url( sort=column.key ) + %> + <th\ + %if column.ncells > 1: + colspan="${column.ncells}" + %endif + > + %if href: + <a href="${href}">${column.label}</a> + %else: + ${column.label} + %endif + <span>${extra}</span> + </th> + %endif + %endfor + <th></th> + </tr> + </thead> + <tbody> + %for i, item in enumerate( query ): + <tr \ + %if current_item == item: + class="current" \ + %endif + > + ## Data columns + %for column in grid.columns: + %if column.visible: + <% + # Link + link = column.get_link( trans, grid, item ) + if link: + href = url( **link ) + else: + href = None + # Value (coerced to list so we can loop) + value = column.get_value( trans, grid, item ) + if column.ncells == 1: + value = [ value ] + %> + %for cellnum, v in enumerate( value ): + <% + # Attach popup menu? + if column.attach_popup and cellnum == 0: + extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i + else: + extra = "" + %> + %if href: + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> + %else: + <td >${v}${extra}</td> + %endif + %endfor + %endif + %endfor + ## Actions column + <td> + <div popupmenu="grid-${i}-popup"> + %for operation in grid.operations: + %if operation.allowed( item ): + <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> + %endif + %endfor + </div> + </td> + </tr> + %endfor + </tbody> + <tfoot> + %if num_pages > 1: + <tr> + <td></td> + <td colspan="100" style="text-align: right"> + Page: + %for page_index in range(1, num_pages + 1): + %if page_index == cur_page_num: + <span style="font-style: italic">${page_index}</span> + %else: + <% args = { "page" : page_index } %> + <span><a href="${url( args )}">${page_index}</a></span> + %endif + %endfor + </td> + </tr> + %endif + %if grid.operations: + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected histories: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + %endif + </tfoot> + </table> +</form> diff -r b819249af24d -r e7b9d15e8e93 templates/history/grid.mako --- a/templates/history/grid.mako Tue Sep 29 17:14:20 2009 -0400 +++ b/templates/history/grid.mako Tue Sep 29 17:57:45 2009 -0400 @@ -303,7 +303,7 @@ %if num_pages > 1: <tr> <td></td> - <td colspan="100" style="font-size: 90%; text-align: right"> + <td colspan="100" style="text-align: right"> Page: %for page_index in range(1, num_pages + 1): %if page_index == cur_page_num: diff -r b819249af24d -r e7b9d15e8e93 templates/my_data.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/my_data.mako Tue Sep 29 17:57:45 2009 -0400 @@ -0,0 +1,13 @@ +<%inherit file="/base.mako"/> + +<%def name="stylesheets()"> + ${h.css( "base" )} +</%def> + +<h2>Available Galaxy Data</h2> + +<ul> + <li><a href='${h.url_for( controller='history', action='list' )}'>Histories</li> + <li><a href='${h.url_for( controller='dataset', action='list' )}'>Datasets</li> +</ul> +

1 0

[hg] galaxy 2798: Fix limiting species in interval2maf tool.
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ff37fcf14bd5 changeset: 2798:ff37fcf14bd5 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 29 21:47:59 2009 -0400 description: Fix limiting species in interval2maf tool. 3 file(s) affected in this change: test-data/interval2maf_3from28way.maf tools/maf/interval2maf.py tools/maf/interval2maf.xml diffs (1344 lines): diff -r e7b9d15e8e93 -r ff37fcf14bd5 test-data/interval2maf_3from28way.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf_3from28way.maf Tue Sep 29 21:47:59 2009 -0400 @@ -0,0 +1,1301 @@ +##maf version=1 +a score=378218.0 +s hg18.chr1 99287304 223 - 247249719 TCCTCTATGCAAGAGTACACTAGCTATTCTGTGGACAGGAGCCAGACAATGTGAGCTGTACATAAGAATTATTTTTGCAGTGTCAAAAGCCATTCTAGGTGGAATCCAAATCACCACTTGCCTTAGACAGACACCCCCTCAGCTTCACTGCAGGTCCAGAGTCAGCCGAGGCCAGAGAGAGAACCACCAGGAGTGGAAGCAACACTCTCTAGGTTCTCTGCAC +s panTro2.chr1 101234886 223 - 229974691 TCCTCTATGCAAGAGTACACTAGCTATTCTATGGACAGGAGCCAGACAATGTGAGCTGTACATAAGAATTATTTTTGCAGTGTCAAAAGCCATTCTAGGTGGAATCCAAATCACCACTTGCCTTAGACAGACACCCCCTCAGCTTCACTGCAGGTCCAGAGTCAGCCGAGGCCACAGAGAGAACCACCAGGAGTGGAAGCAACACTCTCTAGGTTCTCTGCAC + +a score=10640.0 +s hg18.chr1 99287270 34 - 247249719 GCTGTAAGATGCCATGTATTTTGTGATTCTACAA +s panTro2.chr1 101234852 34 - 229974691 GCTGTAAGATGCCATGTATTTTGTGATTCTACAA + +a score=43023.0 +s hg18.chr1 99287229 41 - 247249719 AGGGCCCAGAGGATCTGGCCATGTTCTCATGGCATCATTGA +s panTro2.chr1 101234811 41 - 229974691 AGGGCCCAGAGGATCTGGCCATGTTCTCATGGCATCATTGA + +a score=120618.0 +s hg18.chr1 99287139 90 - 247249719 TCCTTGAAAGGGAAAGACTCTAAAACTTTTCTCTGAATTATGGCCCTGCCACCCCAGCTGGGTTTTTCTCTCAAAGGGAGACAGTAATGA +s panTro2.chr1 101234721 90 - 229974691 TCCTTGAAAGGGAAAGACTCTAAAACTTTTCTCTGAATTACGGCCCTGCCACCCCAGCTGGGTTTTTCTCTCAAAGGGAGACAGTAATGA + +a score=39239.0 +s hg18.chr1 147984545 50 + 247249719 AGAAAAACTTTAGTGGAAACAACCAGTACTTAAAGACCATTTTATGAGGC +s panTro2.chr1 128764240 50 + 229974691 AGAAAAACTTTAGTGGAAACAACCAGTACTTAAAGACCATTTTATGAGGC +i panTro2.chr1 C 0 C 0 + +a score=93901.0 +s hg18.chr1 147984595 35 + 247249719 TGTCATTTACGTATTATCTCTTTTGCTGTTTTTGT +s panTro2.chr1 128764290 35 + 229974691 TGTCATTTACATATTATCTCTTTTGCTGTTTTTGT +i panTro2.chr1 C 0 C 0 + +a score=-5867.0 +s hg18.chr1 99171300 19 - 247249719 CGTGGGGAGAACTGCGCTG +s panTro2.chr1 101114588 19 - 229974691 CGGGGGGAGAACTGCGCTG + +a score=-4312.0 +s hg18.chr1 99171258 42 - 247249719 GGGAAATGACCACCTCGGCCTCGCCGGGGTTCTGCGGACAAA +s panTro2.chr1 101114546 42 - 229974691 GGGAAATGACCACCTCGGCCTCGCCGGGGTTCTGCGGGCAAA + +a score=-5717.0 +s hg18.chr1 99171247 11 - 247249719 CCGGCTAGGGA +s panTro2.chr1 101114535 11 - 229974691 CCGGCTAGGGA + +a score=-26975.0 +s hg18.chr1 99171193 54 - 247249719 GAGCGCCACACGCCCGTGCTTCGCGCCCAAACCGGCCTCACCCGGCGCGGCCAT +s panTro2.chr1 101114481 54 - 229974691 GAGCGCCACACGCCCGTGCTTCGCGCCCAAACCGGCCTCACCCGGCGCGGCCAT + +a score=-60785.0 +s hg18.chr1 99171137 56 - 247249719 ACTAGGGGGACGCTCAGGGCTCGCGGTCCTGAGCGCGGCTGGCCTTTGCGGAAGTG +s panTro2.chr1 101114425 56 - 229974691 ACTAGGGGGACGCTCAGGGCTCGCGGTCCTGAGCGCGGCTGGCCTTTGCGGAAGTG + +a score=151634.0 +s hg18.chr1 148185136 140 + 247249719 acgtctgtaatcccagctactcgtgaggctgatgcaggagaatcacttgaacctgggaagtggaggttgctgtgagccaagattgtgccactgcatttcagcctggctgacagagcaagacttcctctgaaaaaaaaaaa +s panTro2.chr1 128947445 139 + 229974691 acgtctgtaatcccagctactcgtgaggctaatgcaggagaatcacttgaacctgggaagtggaggttgctgtgagccaagattgtgccactgcatttcagcctgggtgacagagcaagacttcctctg-gaaaaaaaaa +i panTro2.chr1 C 0 C 0 + +a score=518150.0 +s hg18.chr10 80123058 56 - 135374737 ACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA +s mm8.chr10 74075614 56 + 129959148 TTAGAGTTGTTGAGGGAATTGACGTGCAACCTCACAGTCAATCAACATCTTTGTAA +s panTro2.chr10 82310642 56 - 135001995 ACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA + +a score=200210.0 +s hg18.chr10 80122998 60 - 135374737 TGTGCCCTTCAGAAGTAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGA +s panTro2.chr10 82310582 60 - 135001995 TGTGCCCTTCGGAAGTAACAAATATGGAAATCACATTTGAACAAAACAAGGAGAATTTGA +s mm8.chr10 74075554 60 + 129959148 TTTGCCCTGCAGAGAAAACAGGCATGAAAATCACACATGACCAGAGCCAGGAAACGTTGG + +a score=136193.0 +s hg18.chr10 80122957 41 - 135374737 AAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTA +s panTro2.chr10 82310541 41 - 135001995 AAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTA +s mm8.chr10 74075513 41 + 129959148 AAAAAACTGCCCACCTGCAGATCCCTCAAAACTACACACGT + +a score=1023171.0 +s hg18.chr10 80122882 75 - 135374737 AAAAGGCATCCTCAGACACGTTAAAAACTTAGCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGA +s panTro2.chr10 82310466 75 - 135001995 AAAAGGCATCCTCAGACATGTTAAAAACTTAGCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGA +s mm8.chr10 74075438 75 + 129959148 AAAAGGGATCCTCAGACATGTGAAAAACTTGGCAGAGCTCGAGAAATCAGTGTCTAACATGTACAGTCACATAGA + +a score=-29743.0 +s hg18.chr10 80122851 31 - 135374737 CAGTGTGTAAAACAGACCCTCAGAGAGAACC +s panTro2.chr10 82310435 31 - 135001995 CAGTGTGTAAAACAGACCCTCAGAGAGAACC +s mm8.chr10 74075407 31 + 129959148 CGCAGTGGGGGGCAGAACCCCACAGACATCC + +a score=121521.0 +s hg18.chr10 80122808 43 - 135374737 GCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGA +s panTro2.chr10 82310392 43 - 135001995 GCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGA +s mm8.chr10 74075364 40 + 129959148 GCCAGAGAAACCA---CGTCTACGACACAGCCACCAGCATCCA + +a score=101339.0 +s hg18.chr10 80122748 60 - 135374737 TTTCTGTCCACAGAGTGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCT +s panTro2.chr10 82310332 60 - 135001995 TTTCTGTCCACAGAGTGTGTCTGTATAACAGGTGTTGAATGCACGACCAACATGATGCCT +s mm8.chr10 74075304 60 + 129959148 ATTCCATCCACAGACAGCATCTCTGCACCAGCTGCTAAATGCACTGCCAGTGCCACACAC + +a score=153575.0 +s hg18.chr10 80122616 132 - 135374737 cctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCCAACA------------ccacctcttctacctccatttccaactcctcttcctccaccacctccttctattccttgccctccacctccttcAGCTTCA +s panTro2.chr10 82310207 125 - 135001995 -------ctACATTTTTTCCACTTTCCATTTCAACGTCTGGTCCCCCAACA------------ccacctcttctacctccatttccaactcctcttcctccaccacctccttctattccttgccctccacctccttcAGCTTCA +s mm8.chr10 74075167 137 + 129959148 ----ccccacaacttgttacattttctcttcccatttctacaccccctacttcttctctacctcttcctcctccactgtcacttcctcctc---ctcctcGGCCACCAGCTCCCCGCCTCTTCCCACAGCCTCCTTCCACGTCC + +a score=-80842.0 +s hg18.chr10 80122576 40 - 135374737 ttgtcctcctccctctcctccttctatccctcttcctctt +s panTro2.chr10 82310184 23 - 135001995 ttgtcctcctccctctcctcctt----------------- +s mm8.chr10 74075144 23 + 129959148 cctttctccccctaaccctcctc----------------- + +a score=15475.0 +s hg18.chr10 80122507 69 - 135374737 tcctccttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctcctttttctctttt +s mm8.chr10 74075096 48 + 129959148 tccgcctcttcctagacct---------------------cccattgcctttaccacttttcctcttcc +s panTro2.chr10 82310115 69 - 135001995 tcctccttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctcctttttctctttt + +a score=-32513.0 +s hg18.chr10 80122465 42 - 135374737 CTCTCCTTCTGCCTGtccccttccccctcctcctcctatttc +s mm8.chr10 74075078 18 + 129959148 CTC------------------------TGctcccctcccaca +s panTro2.chr10 82310073 42 - 135001995 CTCTCCTTCTGCCTGtccccttcctcctccttctcctatttc + +a score=286554.0 +s hg18.chr10 80122411 54 - 135374737 ACCTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAACAT +s panTro2.chr10 82310019 54 - 135001995 ACCTGTTGAAACCGAAAGAAATATGTTTGAAAATTTTGCCCATCCACCAAACAT +s mm8.chr10 74075024 54 + 129959148 AGATACAGAACCAAAAAGGAACTCTTTTGAGATCGCTCCCCATCCACCTAGCAT + +a score=1014462.0 +s hg18.chr10 80122238 173 - 135374737 CCCAGGCCTCACTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTCATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTT +s mm8.chr10 74074848 176 + 129959148 TCTTGGTCTCACTTTTCTTTCTCAACTCTGCCAACGATTTCCAGAGCGGTGGAACTCGGGTCGGAACCTAATGTGGTCACTTCTCCCGCTGACTGCACCTTGGAACTTTCTCCTCCTCTGAGACCCCGTATTTTAAACTCCTTAAGCTCTAAGAGAGAGACTCCCACATGTGCATC +s panTro2.chr10 82309846 173 - 135001995 CCCAGGCCTCACTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTCATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTAAATTCTTCACTCTCTAGGAGAGCGACACCTATTTGTATGTT + +a score=337224.0 +s hg18.chr10 80122083 155 - 135374737 GAATCTGTACAAACAAAAGAGGTAGCAGCAATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATAAGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCTCTCTTCAGACTCTTCATTTTGCTTT +s panTro2.chr10 82309691 155 - 135001995 GAATCTGTACAAACAAAAGAGGTAGCAGCAATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATAAGGCAAGGTGACACACTGATTATGAAAGGAAGAGAACAGTTGAAATCTCTCTCTTCAGACTCTTCATTTTGCTTT +s mm8.chr10 74074696 152 + 129959148 GATGCCACCCAAGCCAGAGAGGTAGCAGCAACGTTCTGCTGGCAACTGAAGATGCCCACGAGTCAGAGAA---AGAAGGGGGACACAGAGACACCCTAATCGTCCAGCAAACAGAGCAGCTGAAATCTCTGTCTTCTGGCTCTTCTTTTTCCTCC + +a score=196272.0 +s hg18.chr10 80122035 48 - 135374737 TGCAGCAGTGGCAAGGCACCAGGCAGAAAGCTGAAAATGAAAACACTG +s panTro2.chr10 82309643 48 - 135001995 TGCAGCAGTGGCAAGGCACCAGGCAGAAAGCTGAAAATGAAAACACTG +s mm8.chr10 74074648 48 + 129959148 TGGTGGAGTGGCAGATCACCAATCAGAGAGCTGAATGCGAAAGCGCCA + +a score=267386.0 +s hg18.chr10 80121994 41 - 135374737 GCTGATGAGGAAAGTTCCAAATAGACCAGAGATCATAGATC +s panTro2.chr10 82309602 41 - 135001995 GCTGATGAGGAAAGTTCCAAATAGACCAGAGATCATAGATC +s mm8.chr10 74074607 41 + 129959148 GCTCATGTGGAAAGCCCCAAACAGGCCAGAGACCATAGACC + +a score=799420.0 +s hg18.chr10 80121885 109 - 135374737 ATTTTGTAGACCCATTTTCACCCAAAATACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGCTGTGGAGTCAGTCAGTCAGCTTACCCAGGAG +s panTro2.chr10 82309493 109 - 135001995 ATTTTGTAGACCTATTTTCACCCAAAGTACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGCTGTGGAGTCAGTCAGTCAGCTTACCCAGGAG +s mm8.chr10 74074498 109 + 129959148 ATTTTGAAGAGCTGTTGGCACCCAGAACACAAGTTAAGAGTCAGTCTCTGAGGGGCCCAAGAGAAAAGATCCAGAGGGTGTGGAATCAGTCTGTGAGCTTTCCTAGGCG + +a score=212883.0 +s hg18.chr10 80121842 43 - 135374737 ATAAGTCAAGTATCAACAAATTCAGACATTTCACAGAGAACAG +s panTro2.chr10 82309450 43 - 135001995 ATAAGTCAAGTATCAACAAATTCAGACATTTCACAGAGAACAG +s mm8.chr10 74074455 43 + 129959148 ATAGGTCAAAGGTCAACAAACTCAGACCTTCAGCCACGAACAG + +a score=804771.0 +s hg18.chr10 80121755 87 - 135374737 AGCAACAAACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAAC +s panTro2.chr10 82309363 87 - 135001995 AGCAACAAACTGAAGGCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAAC +s mm8.chr10 74074368 87 + 129959148 GAGAGCCAGCCTAACCCAGCAAGGACGTTCTCATTTGTTCCTGATGAGGATAACTTAAGTACCCATAATCCCCTTTACATGGAAAGT + +a score=2273365.0 +s hg18.chr10 80121613 142 - 135374737 TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAG +s panTro2.chr10 82309221 142 - 135001995 TATTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAG +s mm8.chr10 74074226 142 + 129959148 TCTTTTCCTTCTCTACCATTTTGAACAAAGCAGGGGAAATAACTCAGTCCCAGAAGACAGGAGCAGTCATCGCGATGGGATGGCCTTTTCCTCCAGTACCACTGAGTCTCATGAGCCAGCTCATGTAGAGGGACCACTTAAG + +a score=591281.0 +s hg18.chr11 18327947 30 - 134452384 GCCTACAAATGGAGTGTTGAGGATATGTAA +s mm8.chr9 46049473 30 + 124000669 GCCTACAAGTGGAGTGTGGAGGATATGTGA +s panTro2.chr11 18640018 30 - 134204764 GCCTACAAATGGAGTGTTGAGGATATGTAA + +a score=887677.0 +s hg18.chr11 18327884 63 - 134452384 TCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTT +s panTro2.chr11 18639955 63 - 134204764 TCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTT +s mm8.chr9 46049410 63 + 124000669 TCCAATGGCTTTGAACAGAAGCGCTTTGCCAGGCTCGCCAGCAAGAAGGCTGTGGAGGAGCTT + +a score=63327.0 +s hg18.chr11 18327883 1 - 134452384 A +s panTro2.chr11 18639954 1 - 134204764 A +s mm8.chr9 46049409 1 + 124000669 A + +a score=156152.0 +s hg18.chr11 116206508 6 + 134452384 ATGCAG +s mm8.chr9 78014961 6 - 124000669 ATGCAG +i mm8.chr9 C 0 C 0 +s panTro2.chr11 115648111 6 + 134204764 ATGCAG +i panTro2.chr11 C 0 C 0 + +a score=204572.0 +s hg18.chr11 116206514 49 + 134452384 CCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC +s panTro2.chr11 115648117 49 + 134204764 CCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC +i panTro2.chr11 C 0 C 0 +s mm8.chr9 78014967 49 - 124000669 CCCCGGACGCTCCTCACTGTGGCCCTCTTGGCTCTCCTGGCATCTGCCC +i mm8.chr9 C 0 C 0 + +a score=27414.0 +s hg18.chr11 18240627 24 - 134452384 ACTAAGAAGCTCAACACCCAGTGA +s panTro2.chr11 18551568 24 - 134204764 ACTAAGAAGCTCAACACCCAGTGA +s mm8.chr9 45981373 24 + 124000669 AGCGAGACTCTGACTGCCCAGTGA + +a score=65817.0 +s hg18.chr11 18240590 37 - 134452384 CTTCAAGGTCAGCTTCCTGAGCGCTCTCGAGGAGTAC +s panTro2.chr11 18551531 37 - 134204764 CTTCAAGGTCAGCTTCCTGAGCGCTCTCGAGGAGTAC +s mm8.chr9 45981336 37 + 124000669 GCTTAAGACCCAAGTCCAGAGTGTGATCGACAAGGCC + +a score=121894.0 +s hg18.chr11 18240544 46 - 134452384 CCGCGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAG +s mm8.chr9 45981290 46 + 124000669 CTGCGCTGGAGGACCTGCGCCATAGTCTGATGCCCATGCTGGAGAC +s panTro2.chr11 18551485 46 - 134204764 CCGCGCTCGAGGACCTCCGCCAGGGCCTGCTGCCCGTGCTGGAGAG + +a score=368735.0 +s hg18.chr11 18240366 178 - 134452384 GACCGCGCGCGCGCCCATGTGGACGCGCTGCGCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGC +s panTro2.chr11 18551307 178 - 134204764 GACCGCGCGCGCGCCCATGTGGACGCGCTGCGCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGC +s mm8.chr9 45981118 172 + 124000669 GACCGCATGCGCACACACGTAGACTCTCTGCGCACACAGCTAGCGCCCCACAGCGAACAGATGCGCGAGAGCCTGGCCCAGCGCCTGGCTGAGCTCAAGA------GCAACCCTACCTTGAACGAGTACCACACCAGGGCCAAAACCCACCTGAAGACACTTGGCGAGAAAGCCAGAC + +a score=97575.0 +s hg18.chr11 18240323 43 - 134452384 CGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGAGATGCGC +s panTro2.chr11 18551264 43 - 134204764 CGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGAGATGCGC +s mm8.chr9 45981075 43 + 124000669 GGAGCTGCAAGGGAGACTGTCCCCTGTGGCTGAGGAATTTCGC + +a score=580950.0 +s hg18.chr11 18240123 200 - 134452384 CAGGAGTTCTGGGATAACCTGGAAAAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGGAGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTCCAAGAGGGCGCGCGCCAGAAGCTGCA +s panTro2.chr11 18551064 200 - 134204764 CAGGAGTTCTGGGATAACCTGGAAAAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGGAGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCCGAGCTCCAAGAGGGCGCGCGCCAGAAGCTGCA +s mm8.chr9 45980875 200 + 124000669 CGGGACTTCTGGGATAACCTGGAGAAAGAAACAGATTGGGTGAGACAGGAGATGAACAAGGACCTAGAGGAAGTGAAACAGAAGGTGCAGCCCTACCTGGACGAATTCCAGAAGAAATGGAAAGAGGATGTGGAGCTCTACCGCCAGAAGGTGGCGCCTCTGGGCGCCGAGCTGCAGGAGAGCGCGCGCCAGAAGCTGCA + +a score=49052.0 +s hg18.chr11 18240102 21 - 134452384 GAACAGCTCGGCCCTGTGACC +s panTro2.chr11 18551043 21 - 134204764 GAACAGCTCGGCCCTGTGACC +s mm8.chr9 45980854 21 + 124000669 GAACGGCTGGGCCCATTGACT + +a score=167437.0 +s hg18.chr11 18240047 55 - 134452384 CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGCTGCGC +s panTro2.chr11 18550988 55 - 134204764 CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGCTGCGC +s mm8.chr9 45980799 55 + 124000669 CCTGAATCTCCTGGAAAACTGGGACACTCTGGGTTCAACCGTTAGTCAGCTGCAG + +a score=-14919.0 +s hg18.chr11 1812377 30 + 134452384 ATGCTCCACCTGCATGGCTGGCAAACCATG +s mm8.chr7 142247071 26 + 145134094 ----CCAACTGGACTACCGTGTAGAAGATG +i mm8.chr7 C 0 C 0 +s panTro2.chr11 1858435 30 + 134204764 ATGCTCCACCTGTATGGCTGGCAAACCACG +i panTro2.chr11 C 0 C 0 + +a score=117382.0 +s hg18.chr12 93909439 1 - 132349534 A +s panTro2.chr12 50116182 1 + 135371336 A +s mm8.chr15 12392656 1 - 103492577 A + +a score=2422168.0 +s hg18.chr12 93909303 136 - 132349534 AAATTGAATCACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAGGGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCTGACAATGATGCTTCTGATGTGGAATA +s panTro2.chr12 50116046 136 + 135371336 AAATTGAATCACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAGGGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCTGACAATGATGCTTCTGATGTGGAATA +s mm8.chr15 12392520 136 - 103492577 AAATCGAATCGCTCTTTGACCACCGGCTATGTTCATGTGGCGCTGCCGACTCGGATGAAGGGAGGTACATTGAGTACATCCGCGTGAAGGGAAGCAACTATCATCTCTCCGACAACGACGCTTCTGACGTGGAGTA + +a score=1478304.0 +s hg18.chr12 93909213 90 - 132349534 GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATCTATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGG +s panTro2.chr12 50115956 90 + 135371336 GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCGTCTACGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGG +s mm8.chr15 12392430 90 - 103492577 GAGCATTCTTCCTCTACGCCGGATTCGCCGCTGTGGGACTGCTTTTTGTCTATGGCTGCCTCCCTGAAACCAAGGGGAAAAAATTGGAGG + +a score=129525.0 +s hg18.chr13 112381694 1 + 114142980 A +s panTro2.chr13 114131566 1 + 115868456 A +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748309 1 + 132085098 A +i mm8.chr8 C 0 C 0 + +a score=39963.0 +s hg18.chr13 112381695 121 + 114142980 TGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGA +s panTro2.chr13 114131567 121 + 115868456 TGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGA +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748310 91 + 132085098 TTTGTTCACCAGAGT----GTCCTGGCCTCCTGCCTATGTGGACTCATTCCCAAGG-ACCAGCCT-TGAAGGACGCA-ATGTAGGG-----CTCCATGGA------------------GGA +i mm8.chr8 C 0 C 0 + +a score=1055.0 +s hg18.chr13 112381816 44 + 114142980 GGGAGGCCCCCGTGATGAATCCCGTGATGAGCCGCCGATCCGAG +s panTro2.chr13 114131688 44 + 115868456 GGGAGGCCCCTGTGATGAATCCCGTGATGAGCCGCTGATCCGAG +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748401 15 + 132085098 GGGAGGTCTGTGTGA----------------------------- +i mm8.chr8 C 0 C 0 + +a score=-16674.0 +s hg18.chr13 112381860 93 + 114142980 CTCAGGCTGCGTCATGGGACCAGCCACAAGGTTGCCTGACC-TATAAAGGTCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTACAGCTGCCAG +s panTro2.chr13 114131732 93 + 115868456 CTCGGGCTGCGTCATGGGACCAGCCACAAGGTTGCCTGACC-TATAAAGGTCACAGGAGTGCCTCAGGGAGACAGAAGCAGTTACAGCTGTCAG +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748416 81 + 132085098 -----------CACTGGGACTTGCCACAGGTCAG--TGATTGTTCAGAGGTCACAGGAGTGCCACCCTCAGGCAGAGTCATCTGTCTTTTCCAG +i mm8.chr8 C 0 C 0 + +a score=1627846.0 +s hg18.chr14 7658261 84 - 106368585 ACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGAGAGGAGCTAA +s panTro2.chr14 7807052 84 - 107349158 ACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGAGAGGAGCTAA +s mm8.chr12 12099869 84 - 120463159 ACCCTGGAGAAACACATGAAAAAGTGGCACGGTGAACACTTGCTGACTAATGATGTCAAAATCGAGCAGGCTGAGAGGAGCTAA + +a score=2813413.0 +s hg18.chr14 7658104 157 - 106368585 GCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGC +s panTro2.chr14 7806895 157 - 107349158 GCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGC +s mm8.chr12 12099712 157 - 120463159 GAGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGC + +a score=1778334.0 +s hg18.chr14 7657988 116 - 106368585 CCGCACCTgggcggcccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACTTGACGGTGCACCG +s panTro2.chr14 7806779 116 - 107349158 CCGCACCTgggcggcccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACTTGACGGTGCACCG +s mm8.chr12 12099596 116 - 120463159 CCTCACCTGGGTGGTCCGGGTCCTGGGAGGCCGAGCTCCAAGGAGGGCCGCCGCAGCGACACATGTGAGTACTGCGGCAAGGTCTTCAAGAACTGTAGCAACCTGACGGTGCACCG + +a score=448798.0 +s hg18.chr14 7657957 31 - 106368585 CCGCAGCGGCACGGCCAGCGGAGGCAGCACC +s panTro2.chr14 7806748 31 - 107349158 CCGCAGCGGCACGGCCAGCGGGGGCAGCACC +s mm8.chr12 12099565 31 - 120463159 GCGCAGTGGCACGGCGAGCGGGGGCAGCACA + +a score=951272.0 +s hg18.chr14 7657896 61 - 106368585 AGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGG +s panTro2.chr14 7806687 61 - 107349158 AGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGG +s mm8.chr12 12099504 61 - 120463159 AGAACGGCAGCCTGCGCTTCTCAACGCCACCCGGGGACCTGCTGGACGGCGGGCTGTCCGG + +a score=2903485.0 +s hg18.chr14 7657646 250 - 106368585 GAGCCCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CGCCGCCAAGCGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCG +s panTro2.chr14 7806437 250 - 107349158 GAGCCCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CTCCGCCAAGCGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCG +s mm8.chr12 12099242 262 - 120463159 GAGCCCTTTCCAGCTCTCTTCCCACGCAAGCCAGCACCGCTGCCCAGCCCTGGGCTCGGTGGTCCCGCGCTGCACGCGGCCAAGCGCATCAAGGTGGAGAAAGACCTGGAGCTGCCACCTGCCGCCCTCATCCCATCTGAGAACGTGTACTCGCAGTGGCTCGTGGGCTACGCAGCATCGCGCCACTTCATGAAGGACCCATTCCTGGGCTTCACGGATGCGCGCCAGTCGCCTTTCGCCACATCGTCGGAACATTCCTCTG + +a score=152242.0 +s hg18.chr14 7657593 53 - 106368585 cgggcgcgggcggcgcggtcaacgggcgcgggggcggCTTCGCGCCAGGCACC +s panTro2.chr14 7806384 53 - 107349158 cgggcgcgggcggcgcggtcaacgggcgcgggggcggCTTCGCGCCAGGCACC +s mm8.chr12 12099189 53 - 120463159 CGGGTGCACCGGGTGCAGTGAACGGGCGCGGCGGGGCCTTCGCGCCAGGCGCA + +a score=564664.0 +s hg18.chr14 7657449 144 - 106368585 AGGTCATGGAGAACGTGGGCCTAGGCGCACTGCCGCAGTACGGCGAGCTCCTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCGTGCggcgggcggcggggacgcgggc---gacgacgacgacgcgggcggctgcggggacg +s panTro2.chr14 7806240 144 - 107349158 AGGTCATGGAGAACGTGGGCCTAGGCGCACTGCCGCAGTACGGCGAGCTCCTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCGTGCggcgggcggcggggacgcgggc---gacgacgacgacgcgggcggctgcggggacg +s mm8.chr12 12099075 114 - 120463159 AGGTGATGGAGGACGCAGGGCTGGGCGCACTGCCGCAGTATGGGGAG------------------AAGCGGGGCGCCTTCCTGAAGCGTGCAGGC---------------GACACGGGTGATGCCGGAGCTGTTGGCTGTGGGGACG + +a score=158337.0 +s hg18.chr14 7657397 52 - 106368585 gggggcggcgcggccAAGGCGCTGGCTGACGAGAAGGCGCTGGTGCTGGGCA +s panTro2.chr14 7806188 52 - 107349158 gggggcggcgcggccAAGGCGCTGGCTGACGAGAAGGCGCTGGTGCTGGGCA +s mm8.chr12 12099026 49 - 120463159 GGGGC---TGCAGCTGCGGCTCTGGCGGATGAGAAGGCTCTGGCCCTGGGCA + +a score=706451.0 +s hg18.chr14 7657293 104 - 106368585 TACTGGAGAACGAGAGCCGGCCCGAGTCGAGCTTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTGGTGGGGTgcccggggtcccgggcgcg +s panTro2.chr14 7806084 104 - 107349158 TACTGGAGAACGAGAGCCGGCCCGAGTCGAGCTTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTGGTGGGGTgcccggggtcccgggcgcg +s mm8.chr12 12098922 104 - 120463159 TGCTGGAGAACGAGAGCCGGCCTGAGTCGAGCTTCAGCATGGACTCGGAGCTGGGCCGTGGCCGCGAGAACGGAGGTGGCGTGCCACCGGGGGTGGCGGGCGCA + +a score=424364.0 +s hg18.chr14 7657246 47 - 106368585 GCCggaggaggaggacgaggaggaggaggaggaggaggaggagCTGC +s panTro2.chr14 7806037 47 - 107349158 GCCggaggaggaggacgaggaggaggaggaggaggaggaggagCTGC +s mm8.chr12 12098878 44 - 120463159 GCCTgaggacga---cgaggacgaggaggaggaagaagaggagCTGC + +a score=0.0 +s hg18.chr14 7657213 33 - 106368585 CCACCACGAGAGCGACCCGTCGCTGGGCCACGA + +a score=1620466.0 +s hg18.chr14 7657080 133 - 106368585 TGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGACGGTGACTTCCG +s panTro2.chr14 7805871 133 - 107349158 TGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGACGGCGACTTCCG +s mm8.chr12 12098715 130 - 120463159 TGAAGACGCACATGCACAAGGCGGGCTCTCTGGCTGGCCGCTCAGACGACGGGCTCTCAGCTGCCAGCTCCCCTGAGCCGGGCACCAGCGAGCTGCCAGGTGA---CCTGAAAGCGGCCGATGGCGACTTCCG + +a score=1419683.0 +s hg18.chr14 7657003 77 - 106368585 TCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACA +s panTro2.chr14 7805794 77 - 107349158 TCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACA +s mm8.chr12 12098638 77 - 120463159 CCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCATGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACA + +a score=2586302.0 +s hg18.chr14 7656851 152 - 106368585 AGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCAGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAG +s panTro2.chr14 7805642 152 - 107349158 AGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCGGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAG +s mm8.chr12 12098489 149 - 120463159 AGTCCCAAGTCCCCGTTCCTCAGCACGCCACCGCTGCCACCCATGCCTGCGGGC---ACACCGCCACCGCAGCCGCCTGCCAAGAGCAAGTCCTGTGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAG + +a score=2626021.0 +s hg18.chr14 7656695 156 - 106368585 GACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAACAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGCAACCCTATGCACCGGCTCCTGAACCCCTTCCAGCCC +s panTro2.chr14 7805486 156 - 107349158 GACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAACAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGCAACCCTATGCACCGGCTCCTGAACCCCTTCCAGCCC +s mm8.chr12 12098333 156 - 120463159 GACCGAGTCATGCGCCTGAACCCCATGGCCATAGACTCTCCTGCCATGGACTTCTCCCGGCGGCTGCGAGAACTGGCCGGCAACAGCTCCACGCCGCCGCCCGTGTCCCCAGGCCGTGGCAACCCTATGCACCGGCTGCTGAACCCTTTCCAGCCC + +a score=2119797.0 +s hg18.chr14 7656589 106 - 106368585 GCCGGGCACGCCGCCTCTCTTCAGTCCCCCGCCGCGCCACCACCTGGACCCGCACCGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTC +s panTro2.chr14 7805380 106 - 107349158 GCCGGGCACGCCGCCTCTCTTCAGTCCCCCGCCGCGCCACCACCTGGACCCGCACCGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTC +s mm8.chr12 12098227 106 - 120463159 GCCAGGTACGCCACCGCTCTTCAGCCCACCGCCACGCCATCACTTGGACCCACACCGCCTCAGTGCAGAGGAGATGGGGCTCGTGGCCCAGCACCCCAGTGCCTTC + +a score=4942642.0 +s hg18.chr14 7656300 289 - 106368585 GTAAAGATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCACGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCTCACGCCGCGGCTCACCATCCCGCCGCCGCTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCCCTTCAACCTGCTGCGCATGACGGGCCCCATCCTGCGGGACCACCCGGGCTTCGGCGAGGGCCGCCT +s panTro2.chr14 7805091 289 - 107349158 GTAAAGATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCACGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCTCACGCCGCGGCTCACCATCCCGCCGCCGCTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCCCTTCAACCTGCTGCGCATGACGGGCCCCATCCTGCGGGACCACCCGGGCTTCGGCGAGGGCCGCCT +s mm8.chr12 12097938 289 - 120463159 GTAAAGATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCCTGGTTCCTGCTGCAGCACGCACAGAACACACATGGCTTCCGAATCTACCTGGAGCCTGGGCCGGCCAGCACCTCGCTCACGCCCAGGCTCACCATCCCGCCACCGCTCGGGCCGGAGACCGTGGCGCAGTCCCCACTCATGAATTTCCTGGGGGACAGCAATCCTTTCAACCTGCTGCGCATGACGGGCCCCATCCTGCGGGACCACCCTGGCTTCGGTGAGGGCCGCTT + +a score=629708.0 +s hg18.chr15 58852016 27 - 100338915 TATAAACACGATTATGTTTCTCACTAA +s mm8.chr2 61086875 27 - 181976762 TATAAACATGATTATGTTTCTCACTAA +s panTro2.chr15 59529448 27 - 100063422 TATAAACACGATTATGTTTCTCACTAA + +a score=373301.0 +s hg18.chr15 58851981 35 - 100338915 TTGGGGAGAGAATTGGATTCAAGCAGCATCCAAAA +s panTro2.chr15 59529413 35 - 100063422 TTGGGGAGAGAATTGGATTCAAGCAGCATCCAAAA +s mm8.chr2 61086840 35 - 181976762 TTGGGGAGAGAATTGGATTCAAGCAGCATCCAAAA + +a score=2237520.0 +s hg18.chr15 58851855 126 - 100338915 ATATTGCTTTAGGGGTATTTGATGTGGTGGTGACGGACCCCTCATGCCCAGCCTCGGTGCTGAAGTGTGCTGAAGCATTGCAGCTGCCTGTGGTGTCACAAGAGTGGGTGATCCAGTGCCTCATTG +s panTro2.chr15 59529287 126 - 100063422 ATATTGCTTTGGGGGTATTTGATGTGGTGGTGACGGACCCCTCATGCCCAGCCTCGGTGCTGAAGTGTGCTGAAGCATTGCAGCTGCCTGTGGTGTCACAAGAGTGGGTGATCCAGTGCCTCATTG +s mm8.chr2 61086714 126 - 181976762 ACATTGCTTTAGGGGTATTTGATGTGGTGGTGACAGACCCCTCATGCCCAGCCTCGGTGCTCAAGTGTGCTGAAGCCTTGCAACTGCCTGTGGTATCACAAGAATGGGTGATCCAGTGCCTCATTG + +a score=562984.0 +s hg18.chr15 41673708 75 + 100338915 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCTCCTGGCTTTGGCCGGAGCGGGGTCT +s panTro2.chr15 40727968 75 + 100063422 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCTCCTGGCTTTGGCCGGAGCGGGGTCT +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121050290 75 + 181976762 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCTGCCCGCCCTGGACTCAGGCTCCTGGCTTTGGCTGGAGCTGGGTCT +i mm8.chr2 C 0 C 0 + +a score=535926.0 +s hg18.chr15 41673783 74 + 100338915 CTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGA---GCTGCCAGTGAACGACGGAGGCTGTATCCCCCGAG +s panTro2.chr15 40728043 74 + 100063422 CTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGA---GCGGCCAGTGAACGACGGAGGCTGTATCCCCCGAG +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121050365 77 + 181976762 CTCACCGCCGGGATTCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGAGGAGACTGTATCCCCCGAG +i mm8.chr2 C 0 C 0 + +a score=1893961.0 +s hg18.chr15 58659665 89 - 100338915 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTATGA +s panTro2.chr15 59329615 89 - 100063422 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTATGA +s mm8.chr2 60921257 89 - 181976762 GTCGAAACTCAGCCTGGGGTCTCTACGACTGGTTCCAAGCCTCCTGGGCCCTGGCATTGCCCGTCAGCATTTTTGGCCACCTATTATGA + +a score=118616.0 +s hg18.chr15 41826029 31 + 100338915 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCGG +s mm8.chr2 121105479 31 + 181976762 ATGCGCTTCAGCTGCCTAGCTCTGCTCCCGG +i mm8.chr2 C 0 C 0 +s panTro2.chr15 40866268 31 + 100063422 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCGG +i panTro2.chr15 C 0 C 0 + +a score=284293.0 +s hg18.chr15 41826060 57 + 100338915 GTGTGGCGCTGCTTCTTGCCGCGGCCCGCCTCGCCGCTGCCTCCGACGTGCTAGAAC +s panTro2.chr15 40866299 57 + 100063422 GTGTGGCGCTGCTTCTTGCCGCGGCCCGCCTCGCCGCTGCCTCCGACGTGCTAGAAC +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121105510 57 + 181976762 GCGTGGCGCTGCTGCTCGCCTCGGCCCGTCTCGCCGCCGCCTCCGATGTGTTGGAAC +i mm8.chr2 C 0 C 0 + +a score=259946.0 +s hg18.chr15 41826117 36 + 100338915 TCACGGACGACAACTTCGAGAGTCGCATCTCCGACA +s mm8.chr2 121105567 36 + 181976762 TGACGGACGAAAACTTCGAGAGTCGCGTCTCCGACA +i mm8.chr2 C 0 C 0 +s panTro2.chr15 40866356 36 + 100063422 TCACGGACGACAACTTCGAGAGTCGCATCTCCGACA +i panTro2.chr15 C 0 C 0 + +a score=478199.0 +s hg18.chr15 41826153 43 + 100338915 CGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG +s panTro2.chr15 40866392 43 + 100063422 CGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121105603 43 + 181976762 CGGGCTCGGCGGGGCTCATGCTAGTCGAGTTCTTCGCCCCCTG +i mm8.chr2 C 0 C 0 + +a score=71812.0 +s hg18.chr16 142908 17 + 88827254 ATGTCTCTGACCAAGAC +s mm8.chr11 32176663 17 + 121798632 ATGTCTCTGATGAAGAA +i mm8.chr11 C 0 C 0 +s panTro2.chr16 146323 17 + 90682376 ATGTCTCTGACCAAGAC +i panTro2.chr16 C 0 C 0 + +a score=320391.0 +s hg18.chr16 142925 78 + 88827254 TGAGAGGACCATCATTGTGTCCATGTGGGCCAAGATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGGAGAG +s mm8.chr11 32176680 78 + 121798632 TGAGAGAGCTATCATCATGTCCATGTGGGAGAAGATGGCTGCTCAGGCCGAGCCCATTGGCACTGAGACTCTAGAGAG +i mm8.chr11 C 0 C 0 +s panTro2.chr16 146340 78 + 90682376 TGAGGGGACCATCATTGTGTCCATGTGGGCCAAGATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGGAGAG +i panTro2.chr16 C 0 C 0 + +a score=1751098.0 +s hg18.chr16 88647174 117 - 88827254 CGGAAATTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCGTCGGGCTTCCCGGGACCGAAGTGCGAAATACAAGTAA +s panTro2.chr16 90501243 117 - 90682376 CGGAAATTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCGTCGGGCTTCCCGGGACCGGAGTGCGAAATACAAGTAA +s mm8.chr17 26007615 117 + 95177420 CGGAAGTTTTCCCGTTCCAGATCCCGAGATAGATACAGGCGCCATCGCAGCCGTTCCCGGAGCCACAGCCGGGGTCACCGCCGGGCTTCCAGGGACCGGAGTACAAAATACAAGTAA + +a score=362047.0 +s hg18.chr16 88647119 55 - 88827254 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCGA +s panTro2.chr16 90501188 55 - 90682376 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCGA +s mm8.chr17 26007560 55 + 95177420 GTCACGCTCCCGGGATCGTCGACGGAGGCGGTCTAGGTCTACCTCCAGAGAGCGG + +a score=119311.0 +s hg18.chr16 244413 4 + 88827254 ATGT +s panTro2.chr16 250030 4 + 90682376 ATGT +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229272 4 - 95177420 ATGA +i mm8.chr17 C 0 C 0 + +a score=805217.0 +s hg18.chr16 244417 122 + 88827254 TGGACCACAAGGACTTAGAGGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAATCCATCAAAAAATGAGGATAACGTGAAAAGCGCGCCTCCACAGTCC +s panTro2.chr16 250034 122 + 90682376 TGGACCACAAGGACTTAGAAGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAATCCATCAAAAAATGAGGATAACGTGAAAAGCGCGCCTCCACAGTCC +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229276 122 - 95177420 TGGACAACAAGGACTTAGAAGCTGAAATACACCCCTTGAAGAATGAGGACAAGAAATCACAGGAAAACCCAGGAAACCTACCAAGAAACGAAGATAACTTGAAGAGCAAGCCTGTGCCTTCC +i mm8.chr17 C 0 C 0 + +a score=459982.0 +s hg18.chr16 244539 41 + 88827254 CGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATT +s panTro2.chr16 250156 41 + 90682376 CGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATT +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229398 41 - 95177420 CGCTTGTCCCGGTGCCGCACAGTGGCATTTTTCCTTTCCCT +i mm8.chr17 C 0 C 0 + +a score=699262.0 +s hg18.chr16 244580 60 + 88827254 GTTTCTCTGCCTTTTTGTGGTGTTCGTCGTCTCATTCGTCATCCCGTGTCCAGACCGGCC +s panTro2.chr16 250197 60 + 90682376 GTTTCTCTGCCTTTTTGTGGTGTTCGTCGCCTCATTCGTCATCCCGTGTCCAGACCGGCC +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229439 60 - 95177420 GTTCACCTGCCTCTTCGTGGTGTTTGTCCTGTCTTTCATCATCCCATGTCCAGACCGTCC +i mm8.chr17 C 0 C 0 + +a score=263619.0 +s hg18.chr16 244640 41 + 88827254 GGCGTCACAGCGAATGTGGAGGATAGACTACAGTGCCGCTG +s panTro2.chr16 250257 41 + 90682376 GGCGTCACAGCAAATGTGGAGGATAGACTACAGTGCCGCTG +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229499 41 - 95177420 CTCCTCACAGGGCACGTGGAAGCTTGACTACAACAATGCAG +i mm8.chr17 C 0 C 0 + +a score=-184929.0 +s hg18.chr16 88567958 28 - 88827254 CCCTGGGGGTGGAGATGGGGTGGCCTAG +s panTro2.chr16 90415110 23 - 90682376 -----GGGGTGGAGATGGGGTGGCCTAG +s mm8.chr17 25938305 28 + 95177420 CCCTGAAGGTGCCGATGGGGAGTAGTAG + +a score=-142475.0 +s hg18.chr16 88567938 20 - 88827254 GAGCCCACAGCGGCTTGTGG +s mm8.chr17 25938285 20 + 95177420 GAGCCTGCAGCAACCAGTTC + +a score=-5251.0 +s hg18.chr16 88567925 13 - 88827254 TCCCACCCCTGTG +s mm8.chr17 25938272 13 + 95177420 GTCTACCCCCAGG + +a score=428688.0 +s hg18.chr16 88567871 54 - 88827254 CGTGTTCCCGTTTACGTGGAGGCCACGGCACTCGAGCCCCAGCCCTGCACTCCT +s panTro2.chr16 90414601 54 - 90682376 CGTGTTCCCAATTACGTGGAGGCCACGGCACTCGAGCCCCAGCCCTGCACTCCT +s mm8.chr17 25938218 54 + 95177420 GCCATTTCCATTCTTGCGGAAGCCTCTGCACTCAAGCCCCAGCCCTGCTCTCCA + +a score=1837801.0 +s hg18.chr18 52330965 74 - 76117153 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA +s panTro2.chr18 53421695 74 - 77261746 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA +s mm8.chr18 74003599 74 - 90736837 ACTATGACTACCTGAATGACTGGGGACCCCGCTTCAAGAAACTGGCGGACATGTACGGCGGTGGTGACGACTGA + +a score=469497.0 +s hg18.chr18 52330944 21 - 76117153 CAAGTAGTGGTGGTGAGCAGG +s panTro2.chr18 53421674 21 - 77261746 CAAGTAGTGGTGGTGAGCAGG +s mm8.chr18 74003578 21 - 90736837 CCAGTAGCGGTGGGGACCAGG + +a score=2266476.0 +s hg18.chr18 52330832 112 - 76117153 GGCCTTAAAGCGGCTGACAATGACCCCACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCCTTGAGCTCCCTTAATTCCT +s panTro2.chr18 53421562 112 - 77261746 GGCCTTAAAGCGGCTGACAATGACCCGACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCCTTGAGCTCCCTTAATTCCT +s mm8.chr18 74003466 112 - 90736837 GGCCTTAAAGCTGCTGACAACGACCCCACGGCGCCACCGTATGACTCCCTCTTAGTCTTTGACTACGAGGGCAGCGGCTCCACGGCTGGCTCCTTGAGCTCCCTCAACTCCT + +a score=1391235.0 +s hg18.chr18 59406881 165 + 76117153 ATGGATTCACTTGGCGCCGTCAGCACTCGACTTGGGTTTGATCTTTTCAAAGAGCTGAAGAAAACAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCATCTTGACTGCAATTGGCATGGTCCTCCTGGGGACCCGAGGAGCCACCGCTTCCCAGTTGGAGGAG +s panTro2.chr18 60102164 165 + 77261746 ATGGATTCACTTGGCGCCGTCAGCACTCGACTTGGGTTTGATCTTTTCAAAGAGCTGAAGAAAACAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCATCTTGACTGCAATTGGCATGCTCCTCCTGGGGACCCGAGGAGCCACCGCTTCCCAGTTGGAGGAG +i panTro2.chr18 C 0 C 0 +s mm8.chr1 108809701 165 + 197069962 ATGGACTCACTAGGCACAGCAGCCACACAGTTCCTGTTTGATCTTTTCAAAGAACTGAATAAAACAAATGATGGCAACGTCTTCTTTTCCCCTGTGGGCATCTCAACAGCCATTGGCATGATCATCCTGGGGACCCGAGGAGCCACTGCTTCTGAGTTACAGAAG +i mm8.chr1 C 0 C 0 + +a score=725586.0 +s hg18.chr18 16661111 110 - 76117153 CATCTCCTTCAACTAATGAAGAGTTCTGTTGTAATCACCCTTTCCTATTCTTCATAAGGCAAAATAAGACCAACAGCATCCTCTTCTATGGCAGATTCTCATCCCCATAG +s panTro2.chr18 17099295 110 - 77261746 CATCTCCTTCAACTAATGAAGAGTTCCGTTGTAATCACCCTTTCCTATTCTTCATAAGGCAAAATAAGACCAACAGCATCCTCTTCTATGGCAGATTCTCATCCCCGTAG +s mm8.chr1 88222178 101 - 197069962 TATCTTTACAGATTACAGAAGATTTCTATTGTGATCATCCATTG---------GTCAAGCACAGTAAGACCAACAGCATCCTCTTCTTTGGCACAATCTCTTCCCCTTAA + +a score=-126872.0 +s hg18.chr18 16661103 8 - 76117153 CGAATTAT +s panTro2.chr18 17099287 8 - 77261746 CGAATTAT +s mm8.chr1 88222173 5 - 197069962 TA---ATT + +a score=1725446.0 +s hg18.chr18 16660844 259 - 76117153 TGATGGAATGGACAAGTTTGCAGAATATGAGAGAGACATGTGTCGATTTACACTTACCTCGGTTCAAAATGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAACCATGGGAATGGTGAATATCTTCAATG---GGGATGCAGACCTCTCAGGCATGACCTGGAGCCACGGTCTCTCAGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGTGGAAGCTGCAGCTGCCACCGCTGTAGTAGTAGT +s panTro2.chr18 17099028 259 - 77261746 TGATGGAATGGACAAGTTTGCAGAATATGAGAGAGACACATGTCGATTTACACTTACCTCGGTTCAAAATGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAACCATGGGAATGGTGAATATCTTCAATG---GGGATGCAGACCTCTCAGGCATGACTGGGAGCCGCGGTCTCTCGGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGCGGAAGCTGCAGCTGCCACCGCTGTAGTAGTAGT +s mm8.chr1 88221911 262 - 197069962 TACTAGAATGGACAAGAGCAGAAAATATGCATATGACCGAGTTGTATTTATCTTTGCCTCGGTTCAAAGTGGAAGAGAAGTATGACCTCTCAGTTCCATTGAAACACATGGGGATGGTTGGCGCCTTTGATCCACAGAAGGCTGACTTCTCTGGCATGAACAGCACTCAAGGTCTTGTGGTGTCTAAAGTTTTACACAAGTCCTTTGTGGAGGTAAATGAAGAGGGAACAGAAGCTGCTGCTACCACGGGGATAAAATCCCA + +a score=231361.0 +s hg18.chr18 16660816 28 - 76117153 CTTGAAGAGAAACTCACTGCTGAGAAAT +s panTro2.chr18 17099000 28 - 77261746 CTTGAAGAGAAACTCACTGCTGAGAAAT +s mm8.chr1 88221883 28 - 197069962 CTTGAAGAACAACTCTCTACTGAAAAGT + +a score=2290170.0 +s hg18.chr18 59600586 154 + 76117153 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAAGGAAATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGCTCAAGATGACTCCCTCT +s panTro2.chr18 60332677 154 + 77261746 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAAGGAAATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGCTCAAGATGACTCTCTCT +i panTro2.chr18 C 0 C 0 +s mm8.chr1 109255795 154 + 197069962 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTGGCTTCGACTTATTCAGAGAGATGGATAGTAGCCAAGGAAATGGAAATGTATTCTTCTCTTCCCTGAGCATCTTCACTGCCCTGACCCTAATCCGTCTGGGTGCTCGAGGTGACTGTGCAC +i mm8.chr1 C 0 C 0 + +a score=17919.0 +s hg18.chr18 59600740 14 + 76117153 CTCAGATTGATAAG +s panTro2.chr18 60332831 14 + 77261746 CTCAGATTGATAAG +i panTro2.chr18 C 0 C 0 +s mm8.chr1 109255949 14 + 197069962 GTCAGATTGACAAG +i mm8.chr1 C 0 C 0 + +a score=177042.0 +s hg18.chr19 59068595 42 + 63811651 ATGCCAGTGACGGTAACCCGCACCACCATCACAACCACCACG +s panTro2.chr19 59561975 42 + 64473437 ATGCCAGTGACGGTAACCCGCACCACCATCACAACCACCACG +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82256 42 - 243910 ATGCCGGTAACAGTAACTCGTACAACCATCACGACTACAACG +i mm8.chr7_random C 0 C 0 + +a score=-114935.0 +s hg18.chr19 59068637 25 + 63811651 ACGTCATCTTCGGGCCTGGGGTCCC +s panTro2.chr19 59562017 25 + 64473437 ACGTCATCTTCGGGCCTGGGGTCCC +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82298 7 - 243910 TCA------------------TCCT +i mm8.chr7_random C 0 C 0 + +a score=340234.0 +s hg18.chr19 59068662 63 + 63811651 CCATGATCGTGGGGTCCCCTCGGGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGC +s mm8.chr7_random 82305 63 - 243910 CCACCACTGTGGGGTCCGCTCGGGCGCTGACCCAGCCGCTGGGCCTCCTCCGCCTCCTGCAGC +i mm8.chr7_random C 0 C 0 +s panTro2.chr19 59562042 63 + 64473437 CCACGATCGTGGGGTCCCCTCGGGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGC +i panTro2.chr19 C 0 C 0 + +a score=295172.0 +s hg18.chr19 59068725 23 + 63811651 TGGTGTCTACCTGCGTGGCCTTC +s mm8.chr7_random 82368 23 - 243910 TAATATCCACCTGTGTGGCTTTC +i mm8.chr7_random C 0 C 0 +s panTro2.chr19 59562105 23 + 64473437 TGGTGTCTACCTGCGTGGCCTTC +i panTro2.chr19 C 0 C 0 + +a score=161030.0 +s hg18.chr19 59068748 38 + 63811651 TCGCTGGTGGCTAGCGTGGGCGCCTGGACGGGGTCCAT +s panTro2.chr19 59562128 38 + 64473437 TCGCTGGTGGCTAGCGTGGACGCCTGGACGGGGTCCAT +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82391 38 - 243910 TCGCTGGTGGCCAGTGTGGGTGCCTGGACAGGGCCCAT +i mm8.chr7_random C 0 C 0 + +a score=1769153.0 +s hg18.chr19 59068786 173 + 63811651 GGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCCTGCTATGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCA +s panTro2.chr19 59562166 173 + 64473437 GGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCCTGCTACGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCA +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82429 173 - 243910 GGGTAACTGGGCCATGTTCACCTGGTGTTTCTGCTTTGCTGTTACCCTCATCATCCTGATTGTGGAGTTAGGTGGACTCCAGGCCCACTTCCCCCTGTCATGGCGAAACTTCCCCATCACCTTTGCCTGCTACGCGGCCCTCTTCTGCCTGTCGTCTTCCATCATCTATCCCA +i mm8.chr7_random C 0 C 0 + +a score=1066893.0 +s hg18.chr19 59068959 145 + 63811651 CCACCTATGTCCAGTTCCTGTCCCACGGCCGTTCGCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGC +s panTro2.chr19 59562339 145 + 64473437 CCACCTATGTCCAGTTCCTGCCCCACGGTCGTTCGCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGC +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82602 145 - 243910 CCACCTATGTGCAGTTCCTAGCTCATGGACGTACCCGGGACCATGCCATCGCTGCCACCACTTTCTCCTGCGTTGCCTGTTTGGCGTATGCCACTGAAGTGGCCTGGACCCGTGCAAGGCCCGGTGAGATCACTGGCTATATGGC +i mm8.chr7_random C 0 C 0 + +a score=925227.0 +s hg18.chr19 59069104 98 + 63811651 CACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTTGCCTGCATCATCTTCGCGTTCATCAGCGACCCCAACCTGTACCAGCACCAGCCGGCCC +s panTro2.chr19 59562484 98 + 64473437 CACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTCGCGTTCATCAGCGACCCCAACCTGTACCAGCACCAGCCGGCCC +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82747 98 - 243910 TACCGTGCCAGGGCTGCTCAAAGTTTTTGAGACCTTCGTAGCCTGTATCATCTTTGCCTTCATCAGTGAGCCGCTCCTGTATAATCAGAAGCCAGCCC +i mm8.chr7_random C 0 C 0 + +a score=900583.0 +s hg18.chr19 59069202 89 + 63811651 TGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTA +s panTro2.chr19 59562582 89 + 64473437 TGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTA +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82845 89 - 243910 TGGAGTGGTGTGTGGCAGTCTATGCCATCTGCTTCATACTAGCAGGGGTGACCATCCTGCTCAACCTGGGGGATTGTACCAACGTGTTG +i mm8.chr7_random C 0 C 0 + +a score=962595.0 +s hg18.chr19 59069291 193 + 63811651 CCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACCGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCG------CAGCCATG------CCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGG +s panTro2.chr19 59562671 193 + 64473437 CCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACTGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCG------CAGCCATG------CCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGG +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82934 205 - 243910 CCCATCCCTTTCCCCACCTTCCTCTCAGGCTTGGCCTTACTCTCTGTTCTCTTTTACGCCACTGCCATCGTCCTCTGGCCCCTCTACCAATTTGATCAGAGATATCAGGGCCAACCCCGCCGTTCAATGGATCCAAGCTGCACTCGTAGTATTAGTTATATACAACCCAACACGGTGTGTTTCTGGGACCGACGACTGGCGGTGT +i mm8.chr7_random C 0 C 0 + +a score=613379.0 +s hg18.chr19 59069484 80 + 63811651 CCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCTGCCCACCTGGTTTTTGTCAAGGTCTAA +s panTro2.chr19 59562864 80 + 64473437 CCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCTGCCCACCTGGTTTTTGTCAAGGTCTAA +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 83139 80 - 243910 CCATCCTGACAGGTATCAACCTGCTGGCATATGTGTCTGATCTGGTGTACTCCACTCGTCTGGTGTTCGTCAAGGTCTGA +i mm8.chr7_random C 0 C 0 + +a score=200956.0 +s hg18.chr19 4575513 112 - 63811651 CCCCCAAGGAGTGACCTATGCTGAGCTAAGCACCAGCGCCCTGTCTGAGGCAGCTTCAGACACCACCCAGGAGCCCCCAGGATCTCATGAATATGCGGCACTGAAAGTGTAG +s panTro2.chr19 4741219 112 - 64473437 CCCCCAAGGAGTGACCTATGCTGAGCTAAGCACCAGCGCCCTGTCTGAGGCAGCTTCAGACACCACCCAGGAGCCCCCAGGATCTCGTGAATATGCGGCACTGAAAGTGTAG + +a score=102826.0 +s hg18.chr19 4575505 8 - 63811651 ACGGCAGA +s panTro2.chr19 4741211 8 - 64473437 ACGGCAGA + +a score=177230.0 +s hg18.chr19 59297998 10 + 63811651 ATGGCTGCGA +s panTro2.chr19 59803934 10 + 64473437 ATGGCTGCGA +i panTro2.chr19 C 0 N 0 +s mm8.chr7 3220484 10 + 145134094 ATGGCCGGGA +i mm8.chr7 C 0 C 0 + +a score=406760.0 +s hg18.chr19 4509426 57 - 63811651 CGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTGGCCAGCCCAGCCTCTGACTGA +s panTro2.chr19 4667557 57 - 64473437 CGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTGGCCAGCCCAGCCTCTGACTGA +s mm8.chr7 141910596 57 - 145134094 CGAGAGCCAGACAAATTGCTACCCTACCCTACCCTGGCCAGCCCACCCTTTGACTAA + +a score=455500.0 +s hg18.chr19 4509363 63 - 63811651 ATTAAGGTTGAGGAAGACTTTGGCTTTGAAGCAGATGAGGCCCTGGATTCCAGTTGGGTTTCT +s panTro2.chr19 4667494 63 - 64473437 ATTAAGGTTGAGGAAGACTTTGGCTTTGAAGCAGATGAGGCCCTGGATTCCAGTTGGGTTTCT +s mm8.chr7 141910533 63 - 145134094 ATTAAGGTTGAGGAAGACTTTGGCTTTGAAGCAGATGAGGCCTTGGATTCAAGTTGGGTTTCC + +a score=-197707.0 +s hg18.chr2 118288583 6 + 242951149 GTCTCG +s mm8.chr1 73674351 6 - 197069962 GAGTCG +i mm8.chr1 I 86 C 0 +s panTro2.chr2b 118424760 6 + 248603653 GTCTCG +i panTro2.chr2b I 7 C 0 + +a score=207197.0 +s hg18.chr2 118288589 79 + 242951149 CTTCCACTTCTCCAGGGGGCGCTGCAAAGATTTTGGTCGCCAAAGATATCACGGTGCGCGCGTCTGGAAGCATTTCCGC +s panTro2.chr2b 118424766 79 + 248603653 CTTCCACTTCTCCAGGGGGCGCTGCAAAGATTTTGGTCGCCAAAGGTATCACGGTGCGCGCGTCTGGAAGCATTTCCGC +i panTro2.chr2b C 0 C 0 +s mm8.chr1 73674357 77 - 197069962 TCCTCCAGTCGCCAGGGGGCGCTGCAGGAAATTCGGTCTCCAAAGGGAACCCAGCTCTCA--CCAGGAACTGTTTCCGC +i mm8.chr1 C 0 C 0 + +a score=1362965.0 +s hg18.chr2 124556947 54 - 242951149 ACA-------GTAAACAC-GTGG----CTTGGATAACACCCATCATCCTATGAAGAATATAGGGAG +s panTro2.chr2b 130071925 54 - 248603653 ACA-------GTAAACAC-GTGG----CTTGGATAACACCCATCATCCTATGAAGAATATGGGGAG +s mm8.chr1 123328978 54 + 197069962 AGCCCTACAAA---GAACCGTGGGCAGTGTGGATGACACTCAGAGCCC---------CATAGGCAG + +a score=44574.0 +s hg18.chr2 220190202 12 + 242951149 atggcttaagct +s panTro2.chr2b 225564868 12 + 248603653 atggcttaagct +i panTro2.chr2b C 0 C 0 + +a score=189610.0 +s hg18.chr2 220190214 28 + 242951149 aattcgaagcaagtatgagccaccaaga +s panTro2.chr2b 225564880 28 + 248603653 aattcgaagcaagtatgagccaccaaga +i panTro2.chr2b C 0 C 0 + +a score=129775.0 +s hg18.chr2 22721476 64 - 242951149 aagaaactgccaaactgttttccagagtggttgtcccattttacctttccactggtaatgtatg +s panTro2.chr2b 22992739 64 - 248603653 aagaaactgccaaactgttttccagagtggttgtcccattttacctttccactggtaatgtatg + +a score=208210.0 +s hg18.chr2 22721289 187 - 242951149 atcactgcaccattcaccattcacccattaaaggacatctgcattgtctcagtttttggctattgcaaataaaactgctataaacatttgtttagtttattgtgtgaatataagtcttcctttctttgtgataaatgcccaagagtgcaattgctgagtcatatggtagttgtatgtttaggttttt +s panTro2.chr2b 22992552 187 - 248603653 atcactgcaccattaaccattcacccattaaaggacatctgcattgtctcagtttttggctattgcaaataaaactgctataaacatttgtttagtttattgtgtgaatataagtcttcctttctttgtgataaatgcccaagagtgcaattgctgcgtcatatggtagttgtatgtttaggttttt + +a score=27396.0 +s hg18.chr2 22721263 26 - 242951149 ttgtgtgcgtcaaaagcttattcttt +s panTro2.chr2b 22992526 26 - 248603653 ttgtttgcgtcaaaagcttattcttt + +a score=336518.0 +s hg18.chr2 22721013 250 - 242951149 Tagtgtcacaaccaaaatattgacatggacggggcaaaattagagaacatttcaatcacaataatggtcccccaagttgcctttttgtagctgtcccctccctaacctctggaaaccactaacccgttctctatttctgcaacactgtcactgtaagaatattgtataaatggaatcatacattgtgtagccttttgagaatggctttttcaactcagtgctattctctggagatacacagtttactgtg +s panTro2.chr2b 22992276 250 - 248603653 Tagtgtcacaaccaaaatattgacatggacggggcaaaattaaagaacatttcaatcacaataatggtcccccaagttgcctttttatagctgtcccctccctaacctctggaaaccactaacccgttctctatttctgcaacactgtcactgtaagaatattgtataaatggaatcatacattgtgtagccttttgagaatggctttttcaactcaatgctattctctggagatacacagtttaccgtg + +a score=86437.0 +s hg18.chr2 22720918 95 - 242951149 tttgagtgtttagtacctttatttttaatataatgtatttacctgtgtttgaatataatgtatttattttttaattatACATTTTATTTTAAGAT +s panTro2.chr2b 22992181 95 - 248603653 tttgagtgtttagtacctttatttttaatataatgtatttacctgtgtttgaatataatgtatttattttttaattatACATTTTATTTTAAGAT + +a score=271443.0 +s hg18.chr2 22720728 190 - 242951149 tctggtgtaaatactcccacaatggccaatttcaaactattagtgtgacatcactgaatgcagaattgggaagaaatgtgccatagcacatcactatagaatatttccaccatacagatataacagacataaataacttccagaatatagacaatagtaaaagtaacaaaataattgggaagtcatgaat +s panTro2.chr2b 22991991 190 - 248603653 tctggtgtaaatactcccacgatggccaatttcaagctattagtgtgacatcactgaatgcagaattgggaagaaatgtgccatagcacatcactatagaatatttccaccatacagatataacagacataaataacttccagaatatagacaatagtaaaagtaacaaaataattgggaagtcatgaat + +a score=197745.0 +s hg18.chr2 22720624 104 - 242951149 ATGCATGAGAAATTCCCTAAC---TTAAAAGCAgt-----cccggtaaaagtttaacaaccatctacgaaaaaaaggaggggaggacctaatttgtagtgtctgctgatttc +s panTro2.chr2b 22991887 104 - 248603653 atgcatgagaaattccctacc---ttaAAAGCAgt-----cccggtaaaagtttaacaaccatctacgaaaaaaaggaggggaggacctaatttgtagtgtctgctgatttc +s mm8.chr1 121613757 108 - 197069962 ATGC-TGTGGAA--CCCTCCTAGGTTGCGGACAGTGGAATGCTGGCAGACACAGAGCAGCCTGTTACGGAGAGGAAAGGGACACCATCTGCTT-GCATTGTCTGCTCATTTC + +a score=50206.0 +s hg18.chr2 22720593 31 - 242951149 TG----GAGTCATCCAGCATCTAAACCCACTTCCT +s panTro2.chr2b 22991856 31 - 248603653 TG----GAgtcatccagtatctaaacccacttcct +s mm8.chr1 121613722 35 - 197069962 CAGCCAGGGTTGGTCGGTACCTAAATGCACTTCTT + +a score=50867.0 +s hg18.chr2 22720539 54 - 242951149 ATAACTGATCTGAGACATTAT-CCATTTTTTGATTGACATTTGCTATTTGGGAGG +s panTro2.chr2b 22991802 54 - 248603653 ATAACTGATCTGAGACATTAT-CCATTTTTTGATTGACATTTGCTATTTGGGAGG +s mm8.chr1 121613670 52 - 197069962 A--A-TGATCTGAGGCCTTTCCCGACTTTTTAGTAAACATTCATTATTTGGGAAG + +a score=357793.0 +s hg18.chr2 22720367 172 - 242951149 ACC---ATCCTGCCATCTCTATGCTGGATATTAAAGAAATGAGATTATAAACAGCCAG-------GATTCCATTCCTCCA-----GCATCTGCTTCAACCACAGTCCACAACAGCCTTTTATAAAATGAGGGAAGCAATGAGGTAGAGAGGAAATAGCCTTAGGAAGAGCC-AGCTTCTTCCTCCTCT +s panTro2.chr2b 22991630 172 - 248603653 ACC---ATCCTGCCATCTCTATGCTGGATATTAAAGAAATGAGATTATAAACAGCCAG-------GATTCCATTCCTCCA-----GCATCTGCTTCAACCACAGTCCACAACAGCCTTTTATAAAATGAGGGAAGCAATGAGGTAGAGAGGAAATAGCCTTAGGAAGAGCC-AGCTTCTTCCTCCTCT +s mm8.chr1 121613496 173 - 197069962 ---aCTCTCATCCCATTCCTTTGCCAAAAATTCAAAAGATGAGATTACAAAAGATGAGAGGATGCAGTGCTCCAGACCCATCCTCAATTCCACCTCAACCACAGGCTGCAGGCCCCTTGAATAAAATAA----------AACACAGGGGG--GAAAGCCTGAGGAAGAGCCCAGGTTCTGTCTCCTCT + +a score=3197.0 +s hg18.chr2 22720323 44 - 242951149 AAAGAGATCTGAGCATTCATAAAACTCCATTTTTTTGTAGTTTT +s panTro2.chr2b 22991586 44 - 248603653 AAAGAGATCTGAGCATTCATAAAACTCCATTTTTTTGTAGTTTT +s mm8.chr1 121613132 41 - 197069962 --AAACAGCTTAGCATCCATAAGCCTCCATATTTTTGTAGCCT- + +a score=51138.0 +s hg18.chr2 22720280 43 - 242951149 GAT--GGAGAAAGATTAGAAACAGCAGTGCCTAGGGAA-AAGTGTA +s panTro2.chr2b 22991543 43 - 248603653 GAT--GGAGAAAGATTAGAAACGGCAGTGCCTAGGGAA-AAGTGTA +s mm8.chr1 121613086 46 - 197069962 AATGGACAGGGGGAATACAAAGGGCATTGACTAAGGGGGAAAGGTC + +a score=1119822.0 +s hg18.chr20 29105541 10 - 62435964 CCTCACCTGA +s panTro2.chr20 29927599 10 - 62293572 CCTCACCTGA +s mm8.chr2 26465210 10 - 181976762 CCTCACATGA + +a score=577225.0 +s hg18.chr20 33513606 69 + 62435964 ATGGAGACAAGAAGCCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTACTGGAAGAGCAG +s mm8.chr2 155653412 66 + 181976762 ATGGAGACAGGGAGCCCCGGGTTG---AACATGAAGCCCCAGTCCTTGCAGCTGGTGCTGGAGGGGCAG +i mm8.chr2 C 0 C 0 +s panTro2.chr20 32554547 69 + 62293572 ATGGAGACAAGAAGCCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTACTGGAAGAGCAG +i panTro2.chr20 C 0 C 0 + +a score=1499195.0 +s hg18.chr20 33513675 117 + 62435964 GTGCTGGCACTACAGCAGCAGATGGCAGAGAATCAGGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCAGGCCAAG +s panTro2.chr20 32554616 117 + 62293572 GTGCTGGCACTACAGCAGCAGATGGCAGAGAATCAGGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCAGGCCAAG +i panTro2.chr20 C 0 C 0 +s mm8.chr2 155653478 117 + 181976762 GTGCTGGCGCTGCAGCAGCAGATGGCCGAGAATCAGGCTGCCTCCTGGCGGAAACTGAAGAACTCCCAAGAGGCCCAGAAGAGACAAGCAACCCTCGTGAGGAAGCTGCAGGCCAAG +i mm8.chr2 C 0 C 0 + +a score=366540.0 +s hg18.chr20 28856457 7 - 62435964 TCCCTAG +s panTro2.chr20 29670686 7 - 62293572 TCCCTAG +s mm8.chr2 26282855 7 - 181976762 TCCCTAG + +a score=182231.0 +s hg18.chr20 28856437 20 - 62435964 ATTTTGGAAGATGGTCTGGT +s panTro2.chr20 29670666 20 - 62293572 ATTTTGGAAGATGGTCTGGT +s mm8.chr2 26282835 20 - 181976762 ATTTTGGAAGATGGTCTGAT + +a score=1173268.0 +s hg18.chr20 33593260 60 + 62435964 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTC +s panTro2.chr20 32635706 60 + 62293572 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTC +i panTro2.chr20 C 0 C 0 +s mm8.chr2 155699581 60 + 181976762 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCTAAGACTCTGGAGGACTTC +i mm8.chr2 C 0 C 0 + +a score=512129.0 +s hg18.chr20 33593320 28 + 62435964 CGGGTCAAGACCTGCGGGGGCGCCACCG +s panTro2.chr20 32635766 28 + 62293572 CGGGTCAAGACCTGCGGGGGCGCCACCG +i panTro2.chr20 C 0 C 0 +s mm8.chr2 155699641 28 + 181976762 CGGGTCAAGACCTGCGGGGGTGCCACGG +i mm8.chr2 C 0 C 0 + +a score=610562.0 +s hg18.chr21 32707032 4 + 46944323 ATGC +s panTro2.chr21 32160918 4 + 46489110 ATGC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 90720131 4 + 98252459 ATGC +i mm8.chr16 I 2 C 0 + +a score=749215.0 +s hg18.chr21 32707036 127 + 46944323 TTCTGCCGGGACGCGCACGCCAACCGCCGACGCCCCAGCCCGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGCCGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCTCCAA +s panTro2.chr21 32160922 127 + 46489110 TTCTGCCGGGACCCGCACGCCAACCGCCGACGCCCCAGCCCGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGCCGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCTCCAA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 90720135 127 + 98252459 TCCTGCCAGGACACCCGCGTCCACCACCCGCGCCCCAATCGGCGCAGAATCAGGGCCTCCGCAGGCAGGTAGAGCCTCCGGGGCAGCTTCTGCGCCTGTTCTACTGCACGGTCCTAGTGTGCTCCAA +i mm8.chr16 C 0 C 0 + +a score=211993.0 +s hg18.chr21 32707163 29 + 46944323 AGAGATCTCAGCGCTCACCGACTTCTCTG +s panTro2.chr21 32161049 29 + 46489110 AGAGATCTCAGCGCTCACCGACTTCTCTG +i panTro2.chr21 C 0 C 0 +s mm8.chr16 90720262 29 + 98252459 AGAGACCTCCGCGCTCACCGATTTCTCTG +i mm8.chr16 C 0 C 0 + +a score=98928.0 +s hg18.chr21 14074369 313 - 46944323 TGGGTGCTTCCTGCATTGCGGGTCTCACGGGGAGGAGACGAGAGTGCCCCTGGTTGAGTCAGGAAAGAATTCTATCTTCACGTCGCTGCCAGCAAATGACCACAGCAGCTTCACGACCTCTGCAGGAACCTATCTTGGTAAAGAAACGGGGCCTATGTGGTGGCCGAGCCTCAGGTGTGGCCGAGCTTCAGGTGTGGCCCTTATGCACAGCACAGCCCAAGCCTGTGGGCACCACTCGCCCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCGAGGTCTGCGTGGCCCTTCAGGGCCGAATCTGA +s panTro2.chr21 14164701 313 - 46489110 TGGGTGCTTCCTGCATTGCGGGTCTCACGGGGAGGAGCCAAGAGTGCCCCTGGTTGAGTCAGGAAAGAATTCTATCTTCACGTCGCTGCCAGCAAATGACCACAGCAGCTTCACGACCTCTGCAGGAACCTATCTCGGTAAAGAAACAGAGCCTATCTGGTGGCTGAGCCTCAGGTGTGGCCGAGCTTCAGGTGTGGCCCTTATGCACAGCACAGCCCAAGCCTGTGGGCACCACTCGCCCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCGAGGTCTGCGTAGCCCTTCAGGGCCGAATCTGA + +a score=108541.0 +s hg18.chr21 14074301 68 - 46944323 ATGGAGCGCCCTCTCATCTGGCACCTTCCTGGCCTCTTTCCCAGGCCCCAGTTCTGTCCATGCAGCTG +s panTro2.chr21 14164633 68 - 46489110 ATGGAGCGCCCTCTCATCTGGCACCTGCCTGGCCTCTTTCCCAAGCCCCAGTTCTGTCCATGCAGCTG + +a score=637432.0 +s hg18.chr21 33321040 72 + 46944323 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCC +s panTro2.chr21 32770081 72 + 46489110 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115258 72 + 98252459 ATGGACTCGGACGCCAGCCTGGTGTCTAGTCGCCCATCGTCCCCAGAACCCGATGATCTTTTTCTGCCCGCC +i mm8.chr16 C 0 C 0 + +a score=158069.0 +s hg18.chr21 33321112 116 + 46944323 CGGAGTAAGGGCAGCAGCGGCAGCGCCTTCACTGGGGGCACCGTGTCCTCGTCCACCCCGAGTGACTGCCCGCCGGAGCTGAGCGCCGAGCTGCGCGGCGCTATGGGCTCTGCGGG +s panTro2.chr21 32770153 116 + 46489110 CGGAGTAAGGGCAGCAGCGGCAGCGCCTTCACTGGGGGCACCGTGTCCTCGTCCACCCCGAGCGACTGCCCGCCGGAGCTGAGCGCCGAGCTGCGCGGCGCTATGGGCTCTGCGGG +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115330 116 + 98252459 CGGAGCAAGGGGGGAAGCAGCAGCGGCTTCACAGGAGGGACTGTGTCCTCGTCCACGCCGAGCGACTGCCCGCCAGAGCTGAGCTCCGAGCTACGAGGGGCCATGGGCGCGTCAGG +i mm8.chr16 C 0 C 0 + +a score=56737.0 +s hg18.chr21 33321228 102 + 46944323 CGCGCATCCTGGGGACAAGCTAGGAGGCAGTGGCTTCAAGTCATCCTCGTCCAGCACCTCGTCGTCTACGTCGTCGGCGGCTGCGTCGTCCACCAAGAAGGA +s panTro2.chr21 32770269 102 + 46489110 CGCCCATCCTGGGGACAAGCTAGGAGGCAGTGGCTTCAAGTCATCCTCGTCCAGCACCTCGTCGTCTACGTCGTCGGCGGCTGCGTCGTCCACCAAGAAGGA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115446 102 + 98252459 CGCGCATCCCGGGGACAAACTGGGCGGCGGTGGCTTCAAGTCATCTTCCTCCAGCACCTCCTCGTCCACGTCCTCGGCGGCCACGTCTTCCACCAAGAAAGA +i mm8.chr16 C 0 C 0 + +a score=1401662.0 +s hg18.chr21 33321330 142 + 46944323 CAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTCCGCGAGGTCATGCCGTACGCACACGGCCCTTCGGTGCGC +s panTro2.chr21 32770371 142 + 46489110 CAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTGCGCGAGGTCATGCCGTACGCACACGGCCCTTCGGTGCGC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115548 142 + 98252459 CAAGAAGCAGATGACTGAGCCCGAGCTGCAGCAGCTGCGCCTGAAGATCAACAGCCGCGAACGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGCGGGAGGTCATGCCTTACGCGCACGGGCCGTCGGTGCGC +i mm8.chr16 C 0 C 0 + +a score=494453.0 +s hg18.chr21 33321472 43 + 46944323 AAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACA +s panTro2.chr21 32770513 43 + 46489110 AAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115690 43 + 98252459 AAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGAAACTACA +i mm8.chr16 C 0 C 0 + +a score=611248.0 +s hg18.chr21 33321515 47 + 46944323 TCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGC +s panTro2.chr21 32770556 47 + 46489110 TCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115733 47 + 98252459 TCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGC +i mm8.chr16 C 0 C 0 + +a score=167373.0 +s hg18.chr21 33321562 184 + 46944323 GAGATCTACGGGGGCCACCACGCTGGCTTCCACCCGTCGGCCTGCGGCGGCCTGGCGCACTCCGCGCCCCTGCCCGCCGCCACCGCGCACCCGGCAGCAGCAGCGCACGCCGCACATCACCCCGCGGTGCACCACCCCATCctgccgcccgccgccgcagcggctgctgccgccgctgcagccg +s panTro2.chr21 32770603 184 + 46489110 GAGATCTACGGGGGCCACCACGCTGGCTTCCACCCGTCGGCCTGCGGCGGCCTGGCGCACTCTGCGCCCCTGCCCGCCGCCACCGCGCACCCGGCAGCAGCAGCGCACGCCGCACATCACCCCGCGGTGCACCACCCCATCctgccgcctgccgccgcagcggctgctgccgccgctgcagccg +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115780 184 + 98252459 GAGATCTACGGGGGTCACCACGCCGGCTTCCACCCATCGGCCTGTGGCGGGCTGGCACACTCGGCGCCTCTACCCACCGCCACGGCGCACCCCGCGGCCGCCGCGCACGCCGCGCACCACCCGGCCGTGCACCACCCCATCCTCCCTCccgcagccgccgccgccgccgcagccgccgccgccg +i mm8.chr16 C 0 C 0 + +a score=235994.0 +s hg18.chr21 33321746 103 + 46944323 cggctgTGTCCAGCGCCTCTCTGCCCGGATCCGGGCTGCCGTCGGTCGGCTCCATCCGTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTgccgcggccgc +s mm8.chr16 91115964 103 + 98252459 cAGCGGTGTCCAGCGCCTCTCTACCGGGCTCCGGGCTGTCCTCGGTCGGATCCATCCGGCCTCCGCACGGCCTGCTCAAGTCACCGTCGGCAGCCGCAGCCGC +i mm8.chr16 C 0 C 0 +s panTro2.chr21 32770787 103 + 46489110 cggctgTGTCCAGCGCCTCTCTGCCCGGATCCGGGCTGCCGTCGGTCGGCTCCATCCGTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTGCCGCAgccgc +i panTro2.chr21 C 0 C 0 + +a score=336560.0 +s hg18.chr21 33321849 74 + 46944323 cccgctggggggcgggggcggcggcAGTGGGGCGAGCGGGGGCTTCCAGCACTGGGGCGGCATGCCCTGCCCCT +s panTro2.chr21 32770890 74 + 46489110 cccgctggggggcgggggcggcggcAGTGGGGCGAGCGGGGGCTTCCAGCACTGGGGCGGCATGCCCTGCCCCT +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116067 74 + 98252459 CCCTCTCGGAGGCGGGGGTGGAGGCAGCGGTGGCAGCGGTGGCTTCCAGCACTGGGGCGGCATGCCGTGCCCCT +i mm8.chr16 C 0 C 0 + +a score=333126.0 +s hg18.chr21 33321923 30 + 46944323 GCAGCATGTGCCAGGTGCCGCCGCCGCACC +s panTro2.chr21 32770964 30 + 46489110 GCAGCATGTGCCAGGTGCCGCCGCCGCACC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116141 30 + 98252459 GCAGCATGTGCCAGGTGCCGCCGCCGCACC +i mm8.chr16 C 0 C 0 + +a score=245579.0 +s hg18.chr21 33321953 40 + 46944323 ACCACGTGTCGGCTATGGGCGCCGGCAGCCTGCCGCGCCT +s panTro2.chr21 32770994 40 + 46489110 ACCACGTGTCGGCCATGGGCGCCGGCAGCCTGCCGCGCCT +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116171 40 + 98252459 ACCACGTGTCGGCTATGGGCGCCGGCACCTTGCCGCGCCT +i mm8.chr16 C 0 C 0 + +a score=-238175.0 +s hg18.chr21 33321993 19 + 46944323 CACCTCCGACGCCAAGTGA +s panTro2.chr21 32771034 19 + 46489110 CACCTCCGACGCCAAGTGA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116211 19 + 98252459 CACCTCCGACGCCAAGTGA +i mm8.chr16 C 0 C 0 + +a score=157215.0 +s hg18.chr21 13199327 2 - 46944323 GA +s mm8.chr16 6787486 2 - 98252459 GA +s panTro2.chr21 13299591 2 - 46489110 GA + +a score=753161.0 +s hg18.chr21 13199283 44 - 46944323 CACTCTGATCTACAAATTTGGAAGAACCGAAGAGCTATGGACCT +s panTro2.chr21 13299547 44 - 46489110 CACTCTGATCTACAAATTTGGAAGAACCGAAGAGCTATGGACCT +s mm8.chr16 6787442 44 - 98252459 CACTCTGATCTACAAATTTGGAAGAACTGAAGAGCTCTGGGCCT + +a score=254771.0 +s hg18.chr22 30120223 42 + 49691432 ctcccatgctgtggaagctttgctattttggtcttcgcaatg +s panTro2.chr22 30280431 42 + 50165558 ctcccatgctgtggaagctttgttattttgctcttcgcaaag +i panTro2.chr22 C 0 C 0 + +a score=154402.0 +s hg18.chr22 19531009 4 - 49691432 CAAT +s panTro2.chr22 19843351 4 - 50165558 CAGT +s mm8.chr11 3149702 4 + 121798632 CAGT + +a score=61287.0 +s hg18.chr22 19530974 35 - 49691432 ATCTCCCAAAATAGGTTAGCCTTGCGGGGAGTGAT +s panTro2.chr22 19843316 35 - 50165558 ATCTCCCAAAATAGGTTAGCCTTGCGGGGAGTGAT + +a score=74044.0 +s hg18.chr22 19530840 134 - 49691432 ttactatccccatgttacatgaggaaactgaggctcataaaggttgggtaatttgttcagggctccacagctaactagaggtggacctgcaatttcaaaccctgatctgcctggtcggagtacttaa-ttacATG +s panTro2.chr22 19843181 135 - 50165558 ttactatccccatgttacatgaggaaactgaggctcataaaggttgggtaatttgttcagggctccacagctaactagaggtggacctgcaacttcaaaccctgatctgcctgGTCGGAGTACTTAAATTACATG + +a score=81981.0 +s hg18.chr22 19530787 53 - 49691432 aagtaccatctccctccattactaacaatcaccaccgcagaaagtaagtgcta +s panTro2.chr22 19843128 53 - 50165558 aagtaccatctccctccattactaacaatcaccaccgcagaaagtaagtgcta + +a score=-1554.0 +s hg18.chr22 19530771 16 - 49691432 acagtatttgacatat +s panTro2.chr22 19843112 16 - 50165558 acagtatttgacatgt + +a score=90207.0 +s hg18.chr22 30665273 17 + 49691432 GGCCTACAGTGGGAGAA +s panTro2.chr22 30838165 17 + 50165558 GGCCTACAGTGGGAGAA +i panTro2.chr22 I 13 C 0 + +a score=642220.0 +s hg18.chr22 30665290 70 + 49691432 AAAGTTAAAATCCTATCTGGGTGACATTATTAATAATTTGTGGACAGGCGGCTGCTCCAGCTCAAGATGG +s panTro2.chr22 30838182 70 + 50165558 AAAGTTAAAATCCTATCTGGGTGACATTATTAATAATTTGTGGACAGGCGGCTGCTCCAGCTCAAGATGG +i panTro2.chr22 C 0 C 0 + +a score=271624.0 +s hg18.chr22 18752166 212 - 49691432 ctgacaaaggagttgtatccggaataaaaagaccaacaggccaactttaaaactcaaaaaaaaaaatgacaCTTGGAGAAGAGCTTCAAGGTGACTGACtagaggtgcccaacattcgtctcctccacaaagaaggagcaaaacagataatcacatgtcaaatagagcatctaacagagaatgctggaattcagcggggaagtgacagaacc +s panTro2.chr22 19062041 173 - 50165558 ctgacaaaggagttgtatctggaataAAAAGACCAACAGGCCAActt---------------------------------------caaggtgactgactagaggtgcccaacattcgtctcctccacaaagaaggagcaaaacagataatcacatgtcaaatagagcatctaacagagaatgctggaattcagcggggaagtgacagaacc + +a score=489900.0 +s hg18.chr5 131424298 81 + 180857866 ATGAGCCGCCTGCCCGTCCTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCA----TGACCCAGACAACGCCC +s panTro2.chr5 133682646 81 + 183994906 ATGAGCCGCCTGCCCGTCCTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCA----TGACCCAGACAACGTCC +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67687980 73 - 121798632 ACCAGCATCCACACCATGCTGCTCCTGCTCCTGATGCTCTTCCACCTGGGACTCCAAGCTTCAATCAGTGGCC------------ +i mm8.chr11 C 0 I 19 + +a score=-86483.0 +s hg18.chr5 131424379 81 + 180857866 TTGAAGACAAGCTGGGTTAACTGCTCTAACATGATCGATGAAATTATAACACACTTAAAGCAGCCACCTTTGCCTTTGCTG +s panTro2.chr5 133682727 81 + 183994906 TTGAAGACAAGCTGGGTTAACTGCTCTAACATGATCGATGAAATTATAACACACTTAAAGCAGCCACCTTTGCCTTTGCTG +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67688072 52 - 121798632 ----CAGAACGTTGA----ATTGCAGCTCTATTGTCAAGGAGATTATAG------GGAAGCTCCCA--------------- +i mm8.chr11 I 19 C 0 + +a score=1522676.0 +s hg18.chr5 49301194 71 - 180857866 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA +s panTro2.chr5 50180989 71 - 183994906 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA +s mm8.chr11 53974612 71 + 121798632 TCTCCAACAAGTGGTTCCATGAGCGAGGACAGGAGTTCTTAAGACCTTGTGGAACAACGGAAGTTGATTGA + +a score=291108.0 +s hg18.chr5 131621326 30 + 180857866 ATGCCCCATTCCGTGACCCTGCGCGGGCCT +s panTro2.chr5 133877364 30 + 183994906 ATGCCCCATTCCGTGACCCTGCGCGGGCCT +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67886277 30 - 121798632 ATGACCCACTCGGTGACCCTGCGCGGCCCT +i mm8.chr11 C 0 C 0 + +a score=990690.0 +s hg18.chr5 131621356 63 + 180857866 TCGCCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGCGCGCCCCTCACCATCTCACGG +s panTro2.chr5 133877394 63 + 183994906 TCGCCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGCGCGCCCCTCACCATCTCACGG +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67886307 63 - 121798632 TCACCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGTGCTCCCCTCACCATCTCGCGG +i mm8.chr11 C 0 C 0 + +a score=519601.0 +s hg18.chr5 49010271 54 - 180857866 CTGCTGACCCCA---GTCCGGT---TGCCCTCCATCCAGGCCATTCCCTGTGCACCGTAG +s panTro2.chr5 49887369 54 - 183994906 CTGCTGACCCCA---GTCCGGT---TGCCCTCCATCCAGGCCATTCCCTGTGCACCGTAG +s mm8.chr11 53619809 60 + 121798632 CTGCTGGGCAACTCTGTGAGGCTGCCGCCCTCTATTCAGGCCATTCCTTGTGCACCATAG + +a score=431236.0 +s hg18.chr5 49010219 52 - 180857866 ACAGCGTGTCTTCACAGATCTGAAGAACATGGATGCCACC---TGGCTGGACAGC +s panTro2.chr5 49887317 52 - 183994906 ACAGCGTGTCTTCACAGATCTGAAGAACATGGATGCCACC---TGGCTGGACAGC +s mm8.chr11 53619754 55 + 121798632 ACAACATGTCTTCACGGAGATGAAGAATATGGACTCCATCATGTGGATGGACAGC + +a score=274608.0 +s hg18.chr5 49010200 19 - 180857866 GGGATATTGGGCTGAGTCT +s panTro2.chr5 49887298 19 - 183994906 GGGATATTGGGCTGAGTCT +s mm8.chr11 53619735 19 + 121798632 GGGACATTGGGATAGGCAT + +a score=3488854.0 +s hg18.chr6 62600248 144 - 170899992 TTGGAAGTTCATGAGGCTAAGCCTGTGCCAGAAAATCACCCACAGTGGGATACAGCAATAGAGGGGGATGAAGACCAGGAGGACAGTGAGGGCTTTGAAGATAGCTTTGAGGAAGAAGAGGAGGAAGAAGAAGATGATGACTAA +s panTro2.chr6 64206236 144 - 173908612 TTGGAAGTTCATGAGGCTAAGCCTGTGCCAGAAAATCACCCACAGTGGGATACAGCAATAGAGGGGGATGAAGACCAGGAGGACAGTGAGGGCTTTGAAGATAGCTTTGAGGAAGAAGAGGAGGAAGAAGATGATGATGACTAA +s mm8.chr10 42517305 144 + 129959148 TTGGAAGTTCATGAGGCCAAGCCTGTGCCAGAAAACCACCCACAGTGGGACACAGCGATAGAAGGTGACGAAGACCAGGAAGACAGTGAAGGATTTGAAGACAGCTTTGAGGAAGAGGAGGAGGAAGAGGAAGGTGGAGACTAA + +a score=673541.0 +s hg18.chr6 108594662 25 + 170899992 ATGAGCAAGCCAGCCGGATCAACAA +s panTro2.chr6 109997450 25 + 173908612 ATGAGCAAGCCAGCCGGATCAACAA +i panTro2.chr6 C 0 C 0 +s mm8.chr10 87687827 25 - 129959148 ATGAGCAAGCCCGCCGGATCAACAA +i mm8.chr10 C 0 C 0 + +a score=2387325.0 +s hg18.chr6 62259841 106 - 170899992 GGTCGCTGGTCATCCTCTGGCACAGAACGAACGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAATAAGACATGCCTGA +s panTro2.chr6 63864488 106 - 173908612 GGTCGCTGGTCATCCTCTGGCACAGAACGAACGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAATAAGACATGCCTGA +s mm8.chr10 42223067 106 + 129959148 GGTCGCTGGTCATCCTCTGGCCCAGAATGAACGTTGTCTTCACATGTTTTTACAGGATGAAATTATAGATAAAAGCTATACTCCATCTAAAATAAGACATGCCTGA + +a score=684735.0 +s hg18.chr6 108722976 80 + 170899992 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATGTGTTGGGTGCGG +s panTro2.chr6 110129713 80 + 173908612 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATGTGTTGGGTGCGG +i panTro2.chr6 C 0 C 0 +s mm8.chr10 87792332 80 - 129959148 ATGGCGGCCTCCTGGTCGCCCTTGGTTACTCTGCGCTCCGCCGCGCGCAGCCGGCTGACTGGGAGAGGTGTTGGGTGCGG +i mm8.chr10 C 0 C 0 + +a score=301881.0 +s hg18.chr6 108723056 59 + 170899992 GGCCTGGGCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGGGAAGCCCTTTTGGAAAG +s panTro2.chr6 110129793 59 + 173908612 GGCCTGGGCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGGGAAGCCCTTTTGGAAAG +i panTro2.chr6 C 0 C 0 +s mm8.chr10 87792412 59 - 129959148 GGCGCGGGTCGTCGCAATCCCTCCTCCGGCCCCTGGCCCTGGGAAACCCCTGTGGAAAG +i mm8.chr10 C 0 C 0 + +a score=77769.0 +s hg18.chr7 113660517 150 + 158821424 acaatatttttacatgtacaaaaggagtgtttaggattcctatagtgaaattaaataa--aaatagtatttcatcatttcatctttatcctctgcatttttactcttgtgtatgtcttatacaaaacagagtatataaaatatttaagtata +s panTro2.chr7 114366363 150 + 160261443 acaatatttttacatgtacaaaaggagcatttaggattcctatagtgaaattaaataa--aaatagtatttcatcatttcatctttatcctctgcatttttactgttgtgtatgtcttatacaaaacagagtatataaaatatttaagtata +i panTro2.chr7 C 0 C 0 +s mm8.chr6 15003289 119 + 149525685 TCAATA-TTTTGCAAGTTCAAAGG---TATTTTGCATTTATATAGCAAAGTTAAACTATTAA-----------------CATATCTGTACT------------TTTTGTATATGTCTGATATAGGACAGATGATATAAAATATTTAGGTTTA +i mm8.chr6 I 216 C 0 + +a score=225170.0 +s hg18.chr7 113660667 18 + 158821424 gtagcacttgtatataaa +s panTro2.chr7 114366513 18 + 160261443 gtagcacttgtatataaa +i panTro2.chr7 C 0 C 0 +s mm8.chr6 15003408 18 + 149525685 GCAGTGCTTTTATATAAA +i mm8.chr6 C 0 C 0 + +a score=109967.0 +s hg18.chr7 42309182 83 - 158821424 AA---ACAGAAAAAATGACAACCTAAAACTGATTTGCTCCTACCGCTTTTGAGAAAAGTAAAAACATAAAATATAATTTTATTCTC +s panTro2.chr7 42970029 83 - 160261443 AA---ACAGAAAAAATGATAACCTAAAACTGATTTGCTCCTACCGCTTTTGAGAAAAGTAAAAACATAAAATATAATTTTATTCTC +s mm8.chr6 131770695 82 - 149525685 CACTGAGGGGGAGGAGGACAACCTGAAATCCATTTGCTCTGATCAGATTTCATGAA----CGGAGATGAAATGTGTTTCTCTCCCA + +a score=102283.0 +s hg18.chr7 42309126 56 - 158821424 CACAGATAGACATA-CCAAATTACAGAGAACAGGTATCTACTGTTCTAAAAACCTGG +s panTro2.chr7 42969973 56 - 160261443 CACAGATAGACATA-CCAAATTACAGAGAACAGGTATCTACTGTTCTAAAAACCTGG +s mm8.chr6 131770639 56 - 149525685 CATAGGTGGGCACAGCCAAATGACAGAAGCTAAGAACCTATTGTTCTAAAA-CCAGC + +a score=19014.0 +s hg18.chr7 42309086 40 - 158821424 CTTTTCTTAGGAACAAGCGCCAGGACTGACTTAAGCATTA +s panTro2.chr7 42969933 40 - 160261443 CTTTTCTTAGGAACAAGCGCCAGGACTGACTTAAGCATTA +s mm8.chr6 131770600 39 - 149525685 GGTTTCTTAGGATCCATTACTGTGAAAGCTGC-TGCATGA + +a score=57850.0 +s hg18.chr7 42309063 23 - 158821424 ATATGTATTTGCCTCTTATTTTC +s mm8.chr6 131770575 23 - 149525685 GTATGTACCTGTCGCCCACTTCC +s panTro2.chr7 42969910 23 - 160261443 ATATGTATTTGCCTCTTATTTTC + +a score=41852.0 +s hg18.chr7 42309040 23 - 158821424 ATTCTTTTTCTTGTACAGAATCA +s panTro2.chr7 42969887 23 - 160261443 ATTCTTTTTCTTGTACAGAATCA +s mm8.chr6 131770552 23 - 149525685 CTTCTCCTGCTTTTACAGTGCGG + +a score=45100.0 +s hg18.chr7 42309035 5 - 158821424 CCTTT +s panTro2.chr7 42969882 5 - 160261443 CCTTT +s mm8.chr6 131770535 5 - 149525685 TAATT + +a score=1784527.0 +s hg18.chr7 116714099 53 + 158821424 T-------GTTTTCGTAAGTTGGAAAAGTTTGACTGGCACAGGAAAG-CATGTCCCATTAA +s panTro2.chr7 117499706 53 + 160261443 T-------GTTTTCATAAGTTGGAAAAGTTTGACTGGCACAGGAAAG-CATGTCCCATTAA +i panTro2.chr7 C 0 C 0 +s mm8.chr6 17948973 59 + 149525685 TTTTATTCATTTTCCTAGCTCAG--AGGTTTGACTGGCACAGGACAGCCAGGTCCTGTTAA +i mm8.chr6 C 0 C 0 + +a score=193794.0 +s hg18.chr7 41875637 246 - 158821424 T-CTATATATTTAAGTCTATGAAAGACATATATATACACATATGTATATGTtaataatatataatatagcctatta-----tatattataatcatatatataaattattatattatttatagtattatatatttatttagaataaatattactatattattatataacatatgttatatacaattataattataatatatattgtattatatattataataATGGGTTAGAGACATATATGTGACATATATA +s panTro2.chr7 42526447 252 - 160261443 TGCTATATATTTAAGTCTATGAAAGacatatatatacacatatgcatatattaataatatataatatagcctattatatattatattataatcatatatataaattattatattatttatagtgttatatgtttatttagaataaatattactatattattatataacatatgttatatacaattataattataatatatgttatattatatattataataataggttaGAGACATATATGTGACATATATA + +a score=4204045.0 +s hg18.chr8 27393549 146 - 146274826 CCCAGCGACAGAGCTGCATGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCCACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATTTTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA +s panTro2.chr8 27880503 146 - 145085868 CCCAGCGACAGAGCTGCATGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCCACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATTTTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA +s mm8.chr15 50593685 146 - 103492577 CCCAGCGACAGAGCTGCATGAATACATTTGCCAGCTGGTTTGGCTACATGCCGCTGATCCATTCTCAGATGAGGCTGGACCCGGTCCTCTTTAAAGACCAAGTCTCAATTCTGAGGAAGAAATACAGAGACATTGAACGACTTTGA + +a score=1001054.0 +s hg18.chr8 27393509 40 - 146274826 ACTTCTCGGGCTTCCCGTTGGGCTGACCCTGACCACTTTG +s panTro2.chr8 27880463 40 - 145085868 ACTTCTCGGGCTTCCCGTTGGGCTGACCCTGACCACTTTG +s mm8.chr15 50593645 40 - 103492577 ACTTCCCGAGCATCCCGCTGGGCCGACCCTGACCACTTTG + +a score=57001.0 +s hg18.chr9 128764156 6 + 140273252 catcaa +s panTro2.chr9 126736437 6 + 138509991 catcaa +i panTro2.chr9 C 0 C 0 +s mm8.chr2 148813766 6 - 181976762 CAGTAA +i mm8.chr2 C 0 C 0 + +a score=16385.0 +s hg18.chr9 128764162 27 + 140273252 actgtatctgtgggccatagttagcct-------------- +s panTro2.chr9 126736443 27 + 138509991 actgtatctgtgggccatagttagcct-------------- +i panTro2.chr9 C 0 C 0 +s mm8.chr2 148813772 31 - 181976762 ----------TGGCACAGGTACACCATTTTCCATGGAGGGA +i mm8.chr2 C 0 C 0 + +a score=76022.0 +s hg18.chr9 11485716 17 - 140273252 TTTTAcaa---gataatgta +s panTro2.chr9 11748557 17 - 138509991 TTTTACAA---GATAATGTA +s mm8.chr2 33142635 20 + 181976762 CTCTAAGAAATGACAATGGC + +a score=169894.0 +s hg18.chr9 11485632 84 - 140273252 aaatatataaatatCAAGGGAATTAAGTAACAACTCTATAATGTTATATTTGAATTGGAAAGATCAGTATTATATTAGTCAAAT +s panTro2.chr9 11748473 84 - 138509991 aaatatataaatatCAAGGGAATTAAGTAACAACTCTATAATGTTATATTTGAATTGGAAAGATCAGTATTATATTAGTCAAAT +s mm8.chr2 33142562 73 + 181976762 AAATACAAGAAAATCAAGATCCTTAGGGAACATCAGGATAAGGACAGGTAAGAGCTGGGAAGAGTGACT-----------CACC + +a score=100082.0 +s hg18.chr9 11485610 22 - 140273252 CCAAAATTGTCACTGtaaaata +s panTro2.chr9 11748451 22 - 138509991 CCAAAATTGTCACTGtaaaata +s mm8.chr2 33142540 22 + 181976762 CTAAAACTGCCATTGTCAAATA + +a score=31644.0 +s hg18.chr9 11485572 38 - 140273252 atG-----------ACGGGATAATAT----AAAGTAAG----TAATGTTGCTAGGAA +s panTro2.chr9 11748413 38 - 138509991 atG-----------ACGGGATAATAT----AAAGTAAG----TAATGTTGCTAGGAA +s mm8.chr2 33142484 56 + 181976762 GAGTGCACAGGCACGAGTTAGAACAACGCAGGAA-AAGTAACCAGTATTGTTAGGAA + +a score=59361.0 +s hg18.chr9 11485526 46 - 140273252 TAGTAGTAATATTCGtattattat---------------------ttttaaattattttacata----tat +s panTro2.chr9 11748367 46 - 138509991 TAGTAGTAATATTCGtattattat---------------------ttttaaattattttacata----tat +s mm8.chr2 33142413 71 + 181976762 TGACAATAATGGCCTTGCTATTTTAAAGCACCCAGCCCACCTCCACCCAGTGTGCATGCACATACATATGT + +a score=132295.0 +s hg18.chr9 11485487 39 - 140273252 TGCAAG---------AAAATGTTAAAATTTGACCAGCAGTCTACTGCT +s panTro2.chr9 11748328 39 - 138509991 TGCAAG---------AAAATGTTAAAATTTGACCAGCAGTCTACTGCT +s mm8.chr2 33142362 48 + 181976762 TGCAAACAGAACCACAAAGTGGGAAACTTGAACCTGCAGTCGGCCAGG + +a score=57825.0 +s hg18.chr9 11485468 19 - 140273252 AAGAAGTAAAAGAACTAAC +s panTro2.chr9 11748309 19 - 138509991 AAGAAGTAAAAGAACTAAC +s mm8.chr2 33142345 17 + 181976762 CAGAAGAAAGGGAAC--AC + +a score=350567.0 +s hg18.chr9 11485308 160 - 140273252 caggtactgGGATTACAACAGGGTATCTCAGTATGCAGACCCTCTAGAACCAAATTAGCATAACCCTCCTTTTCTGTCCTGGTGCTTCCAAAGACCTTTAAGGGAAAAGTCCAGGGGAGAGGCCC---ACT--TGGGTATGTAAGTAGTAGGAAAGAGAGAAGAC +s mm8.chr2 33142195 150 + 181976762 CAGGTACTGAGATTACACCAGGGCCTCTTGGAGTACAGACCTCC--------------AAAAACCAGCTGCCTGTGACCACCTTCTTCTGAAAACCT-TAGAGGCAAAGAAAAGATGGAAGGCCCAACCCATCAAGAGGTGTGAGAGGAAGGAGGGAGAGACAAC +s panTro2.chr9 11748149 160 - 138509991 caggtactgGGATTACAACAGGGTATCTCAGTATGCAGACCCTCTAGAACCAAATTAGCATAACCCTCCTTTTCTGTCCTGGTGCTTCCAAAGACCTTTAAGGGAAAAGTCCAGGGGAGAGGCCT---ACT--TGGGTATATAAGTAGTAGGAAAGAGAGAAGAC + +a score=-38935.0 +s hg18.chr9 11485292 16 - 140273252 attatgta-ctg-tgttc +s panTro2.chr9 11748133 16 - 138509991 attatgta-ctg-tgttc +s mm8.chr2 33142179 16 + 181976762 --TGAGCAGCTGCTACTC + +a score=73778.0 +s hg18.chr9 11485257 35 - 140273252 CATCCATTCACACtccactcattcaacaaatattt +s mm8.chr2 33142146 33 + 181976762 GTATTGGCCCTTCTCCACTCAG--GACAGATCCCC +s panTro2.chr9 11748098 35 - 138509991 CATCCATTCACACtccactcattcaacaaatattt + +a score=368197.0 +s hg18.chr9 11485084 173 - 140273252 GAATCTTCAAAAGGCTGAGCTCACCAGGAAATACCC-------TTGCTTTGCGGGAAGTGGTTACACCACAAAACAAGACACCCTGGTAATATCGCTCCTTTGGTTGGCACACGCCCTCGCTTGGCAGTGTGCCTAAACACAGCCAGATAATGTTCTGCTATGGCGCTTCCCCTTTCAGG +s panTro2.chr9 11747926 172 - 138509991 GAATCTTCAAAAGGCTGAGCTCACCAGGAAATACCC-------TTGCTTTGCGGGAAGTGGTTACACCAC-AAACAAGACACCCTGGTAATATCGCTCCTTTGGTTGGCACACCCCCTCGCTTGGCAGTGTGCCTAAACACAGCCAGATAATGTTCTGCTATGGCGCTTCCCCTTTCAGG +s mm8.chr2 33141997 149 + 181976762 AAATCTCCAAAAGGCTGAGCCCACCAGGCAAAACCCCTCTTTTTTTCTTTGGGAAAAGTGACCAC----------TGCGCACCCAGTAGACACTGCTCCT-GAGCTGTCCTGTCCTG--------------------AGTCAGTCAGAAAACACTGTGCCAAGATGCTTGCCCTCACTGG + +a score=735006.0 +s hg18.chr9 11484882 202 - 140273252 AGAGTCACCAGGGGACAGGGCAGTTATGGTTCCATATTTGTAACTTCCATTTTCCTTACTCTCTGCCAATCCTTAACTCACCGTCTGCCTGGCTTCCTCTAAGCCCTGAAATGATGTTCTTTGTGGTCCCCCTTGCAGAAACCAGCAGAAGTCATGAAAAGCCACAGCTCCACCCTCAGTTATCAACTGCATTTGGAAATGT +s panTro2.chr9 11747724 202 - 138509991 AGAGTCACCAGGGGACAGGGCAGTTATGGTTCCATATTTGTAACTTCCATTTTCCTTACTCTCTGCCAATCCTTAACTCACCGTCTGCCTGGCTTCCTCTAAGCCCTGAAATGATGTTCTTTGTGGTCCCCCTTGCAGAAACCAGCAGAAGTCATGAAAAGCCACAGCTCCACCCTCAGTTATCAACTGCATTTGGAAATGT +s mm8.chr2 33141834 163 + 181976762 -----TAGCAGGGATCAGCACAATCGTG-TCCCATGCTTGTGACCTCCACATTCCTTATACTCTGCCAGTCC------------------------TCCTGAGTCCTGGGATGAGGCG--CTGTGGTTACCCCA-CAGAGAAGAGCACAAGTCCTAGT--GCTACA-TTCCAGCCCCAGCTGTGGGAGCCACT---GAATTC + +a score=440472.0 +s hg18.chr9 11484776 106 - 140273252 GGGGTTCTAGGCCACAACTTGTAAGTTCAACACAGCTGTGAGATATTATGCTACAAAGCTATATCTGCATTAATACACCAATTTTTGATAAACTTGGTCACTCGTT +s panTro2.chr9 11747618 106 - 138509991 GGGGTTCTAGGCCACAACTTGTAAGTTCAACACAGCTGTGAGATATTATGCTACAAAGCTATATCTGCATTAATACACCAATTTTTGATAAACTTGGTCACTCGTT +s mm8.chr2 33141754 80 + 181976762 AG-------------------------CAGCCTAGCTATAAGCAGA-ATGCCACAGAATTACATGTACGTTAAGTTGCCAGCTCTTTATAAAACTGGTCACTTATT + +a score=157210.0 +s hg18.chr9 11484715 61 - 140273252 CCTGGCAGCCAGGAATCCACCCAGGAATCTACCCTGCAACCCAATCCACCACAGTGGCAAT +s mm8.chr2 33141702 52 + 181976762 CCTGGCAGGCAGGAGTCTAACCAGA------G-CTGTCACCCAGTT-ATCCAGGTC-CAAC +s panTro2.chr9 11747557 61 - 138509991 CCTGGCAGCCAGGAATCCACCCAGGAATCTACCCTGCAACCCAATCCACCACAGTGGCAAT + +a score=-50628.0 +s hg18.chr9 11484601 114 - 140273252 GTAAGGAGCTCTGGTAGAGACAAAACACCACCTTGAAAACATACCCTTTTAGAAGGCTGCTACCACCAGGACCTTCAGACAGACCTCCTTTACAATGCAGCCCTTGCCCCAAGC +s panTro2.chr9 11747443 114 - 138509991 GTAAGGAGCTCTGGTAGAGACAAAACACCACCTTGAAAACATACCCTTTTAGAAGGCTGCTACCACCAGGACCTTCAGACAGACCTCCTTTACAATGCAGCCCTTGCCCCGAGC +s mm8.chr2 33141592 110 + 181976762 GTAGGGAATACTG-TGGACACAAAATGCTATGCCAAAACATGCCAGGTCAAGCAGGATGCAGCCACCAGGACCCTCAAACAAAG-CCCTTCATGAGGTAGCGTCA--CCCGAGC + +a score=125989.0 +s hg18.chr9 11484506 95 - 140273252 ACAAAAACAGTTCTGACATTTAGACCAGCCTCTGAGACACTGCTGCGCCTTCAACTCCATAGGCTGGGAACTGGACATACTGACAGACAGATGTG +s panTro2.chr9 11747348 95 - 138509991 ACAAAAACAGTTCTGACATTTAGACCAGCCTCTGAGACACTGCTGCGCCTTCAACTCCATAGGCTGGGAACTGGACATACTGACAGACAGATGTG +s mm8.chr2 33141545 47 + 181976762 -----------------------------CTCTGAGGAGCTGTAGGAGCCTCCGTTCTGTG------------AGTATGA-------CAGACTTG + +a score=128122.0 +s hg18.chr9 11484395 111 - 140273252 AGCTCAGCTCTGACAGAACCCTGGGCTGAATAAAGCACAGGCTGTGCCCATTTTCAGCACATTCTAAGAACAGCAGTTTCCCCTTGATGCTGCTCCATGCTAAAACTAATG +s panTro2.chr9 11747237 111 - 138509991 AGCTCAGCTCTGACAGAACCCTGGGCTGAATAAAGCACAGGCTGTGCCCATTTTCAGCACATTCTAAGAACAGCAGTTTCCCCTTGATGCTGCTCCATGCTAAAACTAATG +s mm8.chr2 33141446 99 + 181976762 AGCTCAACTCTGATAGGGTCATGGGCTAAGTACAGCCAAGGCCATGTCCATTTCCAGCTCAGTTTGAGAACAG-AGATCCACCATGCTGGGGTCTGGTGC----------- + +a score=88798.0 +s hg18.chr9 11484289 106 - 140273252 acttgtcctaagtctccaagctag-aggggtgaggctgtgactcaacctcagcttcatcagatcaaagttcatgctcttCAAGCTGTGTGGCTTTAACAGACCCAGC +s panTro2.chr9 11747131 106 - 138509991 acttgtcctaagtctccaagctag-aggggtgaggctgcgactcaacctcagcttcatcagatcaaagttcatcctcttCAAGCTGTGTGGCTTTAACAGACCCAGC +s mm8.chr2 33141368 78 + 181976762 GT----CCAGCATC--TTAGCTGGGATGAGAGCAGCCACA-CCCAT-CCCAGCTCTGACAGAT-------------------GTTATATATAGTTATTAAGC--AGT + +a score=128280.0 +s hg18.chr9 11484174 115 - 140273252 gctttgtacaggcaccgcgctaagttcttacatgcccactgtaaggtaaaagc---------tatgacttccaccccccgccaactttacacatgagaaaatcaaggcataaagaaaatacatg +s panTro2.chr9 11747016 115 - 138509991 gctttgtacaggcaccgtactaagttcttacatgcccactgtaaggtaaaagc---------tatgatttccaccccccgccaactttacacatgagaaaatcaaggcataaagaaaatacatg +s mm8.chr2 33141283 85 + 181976762 ---------------------------CTGGGTAGCTGCTGTGAGTTcaaaacaaaacaaaacaaaaTCACATCTC-------CCAT---GCACAAGGAAACTATAAGATAATGAGTAAGGA-- + +a score=175099.0 +s hg18.chr9 11484116 58 - 140273252 ACAGTGCCTATTCAAACTATACATTGGTGAaatgatagccacgcatgactaggagctt +s panTro2.chr9 11746958 58 - 138509991 ACAGTGCCTATTCAAACTATACACTGGTGAaatgatagccacgcatgactaggagctt +s mm8.chr2 33141234 49 + 181976762 ACAGAGCCAGCTCAGACTGAGCAGCAG-----CAATAACCACAAATGACTGACA---- + +a score=294709.0 +s hg18.chr9 128882427 96 + 140273252 aacacattgcttgttgtaaaaattattcacactgaaaagaagtttataaagtaaaaagtgaatgtgccattcttcttctcccactttccagaggca +s panTro2.chr9 126860344 91 + 138509991 AACACATTGCTTGTTGTAAAAATTATTCACACT-----GAAGTTTATAAAGTAAAAAGTGAATGTGCCATTATTCTTCTCCCACTTTCCAGAGGCA +i panTro2.chr9 C 0 C 0 +s mm8.chr2 148901693 74 - 181976762 -------------CTGTGGAGATCATCCACATTACAAAGAAGTCTATAAAGTAAAATGTGAAAGT--CGCTCTGCCCCTCC-------CTCCGGCG +i mm8.chr2 C 0 C 0 + +a score=-107864.0 +s hg18.chr9 11336020 3 - 140273252 ACT +s panTro2.chr9 11593518 3 - 138509991 ACT +s mm8.chr2 33023385 3 + 181976762 ACT + +a score=-82513.0 +s hg18.chr9 11335985 35 - 140273252 ACGTGTCAATCTCCCTCCCCAAAGAGGGAGAGAGG +s panTro2.chr9 11593483 35 - 138509991 GCGTGTCAATCTCCCTCCCCAGAGAGGGAGAGAGG +s mm8.chr2 33023361 24 + 181976762 ---------TCTTCCTTCCC--ACCAGGAGGGAGG + +a score=80475.0 +s hg18.chr9 11335945 40 - 140273252 ACCAGTTTCTATGTTCAATGTGACCCAAACTCCAGGGGCT +s panTro2.chr9 11593443 40 - 138509991 ACCAGTTTCTATGTTCAATGTGACCCAAACTCCAGGAGCT +s mm8.chr2 33023351 10 + 181976762 GCCTGCCTCT------------------------------ + +a score=-9994.0 +s hg18.chr9 11335933 12 - 140273252 CTAGAA---------------------------ACAGCC +s panTro2.chr9 11593431 12 - 138509991 CTAGAA---------------------------ACAGCC +s mm8.chr2 33023313 38 + 181976762 -CAGAACAGTTTACGCTCCGTGAGACCTGCGGGCCAGCT + +a score=-18269.0 +s hg18.chr9 11335906 27 - 140273252 GAGTTTCTGCTTTCAGACATCTCTATA +s panTro2.chr9 11593404 27 - 138509991 GGGTTTCTGCTTTCAGAAATCTCTATA +s mm8.chr2 33023295 18 + 181976762 AAGCCTCTGCAG-CAGAAA-------- + +a score=163495.0 +s hg18.chr9 11335807 99 - 140273252 ATGTGGGCCCATCTTGCAAGGGCCACAGAGACAGGAATGAGAGGGTGGAGCCCACTTCTTCCCAGATACTCAAGTCCTTCCAAGGCCTTGTGACCCCAT +s panTro2.chr9 11593305 99 - 138509991 ATGTGGGCCCATCTTGCAAGGGCCACAGAGACAGGAATGAGAGGGTGGAGCCCACTTCTTCCCAGATACTCAAGTCCTTCCAAGGCCTTGTGACCCCAT +s mm8.chr2 33023200 95 + 181976762 ATCTTGGTCT-CCTGGCAAGACCACAGAGAATTAGATAGTGAGAATGGACCCCACCTCTTCTCAGCGACCCAAGTCCACT---GTCCTACAGGCTTCCA + +a score=100797.0 +s hg18.chrX 122745047 18 + 154913754 accatcaagaaagtaaaa +s panTro2.chrX 123190863 18 + 155361357 actatcaagaaagtaaaa +i panTro2.chrX C 0 I 759 + +a score=0.0 +s hg18.chrX 122745065 483 + 154913754 agacaacctacagaatgggagaaaatatttgcaaaccatatatctgacaagggacttttatctagaatgtataaccttaacattcaataatctttaaaaaaaaaaaagcccaatttgtttttttgtttttttttttgtttgttttttgttttttgtttttttttgagacggaggctcactctgtcacccaggctggagtgcagtggtgcgatctcagctcactgcaagctccgcctcccaggttcacgccattctcctgcctcagcctcccgagtagctgggactacaggcgcctgccaccacgcccagctaattttttgtatttttagtagagatggggtttcaccgtgttagccaggatggtctcgatctcctgacctcttgatctgcccaccttggcctcccaaagtgctgggattacaggtgagagccaccacgcccagccaaaaaaaaaagcccaattttcaaaaaggggcaaagggg + +a score=17937.0 +s hg18.chrX 122745548 189 + 154913754 ccgggcacggtggctcacgcctgtaatctcagcactttgggaggccaaggcagggggatcaggaggtcaggagttcgagaccagcctggccaaagcgaccagcctggccaacatggtgaaaccctgtctctactaaaaatacaaaaattagccgggcatggtggcagtacctgtaatcccagctactcg +s panTro2.chrX 123191640 189 + 155361357 ccgggcacggtggctcacgcctgtaatctcagcactttgggaggccaaggcagggggatcaggaggtcaggagttcgagaccagcctggccaaagggaccagcctggccaacatggtgaaaccctgtctctactaaaaatacaaaaattagccgggcatggtggcagtacctgtaatcccagctactcg +i panTro2.chrX I 759 C 0 + +a score=88563.0 +s hg18.chrX 122745737 187 + 154913754 ggaggctgaggcaggagaattgcttgaacccaggaggcagaggttgcagtaagctgagattgccccattgcactccagcctgggcaacagagtgagactcctactcaaaaaaaaaaaaaaaaaaaa-gttggcggatgcggggacagcaaagggcttaagtagacatttcttcaaagaagatatacaa +s panTro2.chrX 123191829 188 + 155361357 ggaggctgaggcaggagaattgcttgaacccaggaggcagaggttgcagtaagctgagattgccccattgcactccagcctgggcaacagagtgagactcctactcaaaaaaaaaaaaaaaaaaaaaGTTGGCAGATGCGGGGACAgcaaagggcttaagtagacatttcttcaaagaagatatacaa +i panTro2.chrX C 0 C 0 + +a score=60355.0 +s hg18.chrX 2264558 232 - 154913754 ctatctgggctcactgccagctccgcctcccgggttcacgccattcttctgcctcagcgtcccgagtagctgggactataggcgcccgccaccgcgcccggctaaatttttgtatttttagtagagatggggtttcaccctgttagccaggatggtctcgacctcctgacctcgtgatctgcccgcctcaccctcccaaagtgctgggatgccaggcgggagcccccgcgcc +s panTro2.chrX 2180049 232 - 155361357 ctctctgggctcactgccagctctgcctcccgggttcatgccattcttctgcctcagcgtcccgagtagctgggactacaggcgcccgcccccgcgcccggctaaatttttgtatttttagtagagatggggtttcaccctgttagccaggatggtctcgacctcctgacctcgtgatctgcccgcctcaccctcccaaagtgctgggattacaggcgtgagccaccgtgcc + +a score=-54866.0 +s hg18.chrX 152691446 7 + 154913754 TCAGAAC +s panTro2.chrX 153225439 7 + 155361357 TCAGAAC +i panTro2.chrX C 0 C 0 +s mm8.chrX 70018668 2 + 165556469 -----GC +i mm8.chrX C 0 C 0 + +a score=-88144.0 +s hg18.chrX 152691453 18 + 154913754 CGGAGGGCCTTGGGCATG +s mm8.chrX 70018670 18 + 165556469 TGGAGGGTCTTGAGGATG +i mm8.chrX C 0 C 0 +s panTro2.chrX 153225446 18 + 155361357 CGGAGGGCCTTGGGCATG +i panTro2.chrX C 0 C 0 + +a score=2270241.0 +s hg18.chrX 2219694 31 - 154913754 AGGCCAACCTGCGTAGCATGAGCTTGGGGTT +s panTro2.chrX 2133314 5 - 155361357 --------------------------GGGTT +s mm8.chrX 95535223 31 - 165556469 AGGCCAACCTGCGTAACATGAGCTTGGGGTT + +a score=-439513.0 +s hg18.chrX 2219662 32 - 154913754 AAGCCCTCACCCCCGCCACCGGGTCCAGGTCA +s mm8.chrX 95535191 32 - 165556469 AAGCCCCTGCCCCTGCCCCCACATTCAGGTCA + +a score=-528572.0 +s hg18.chrX 2219603 59 - 154913754 TGGCCCCACCCGCCCCTGGACAGAGCCCGCCCAGGGTGCGATGGGGGCAGGTCTGTGGC +s mm8.chrX 95535133 58 - 165556469 TGGCTCCTGAC-CTCAGGGCCTGATCCCACACCACCTGTATTAGCAATGGGTCAGAGGT + +a score=-746000.0 +s hg18.chrX 2219540 63 - 154913754 CTTTGTGCCTGTGTCCCTGCTGAGGACATCTCACTTTCCTTCCC--CCCACCTGCTGGGGCTTCC +s mm8.chrX 95535080 53 - 165556469 ------------GGCCCTGGTGAGGATAGTCCTCAGATCTTCTCTGAGCCCACTCCTGGAGTTCC + +a score=-199075.0 +s hg18.chrX 2219515 25 - 154913754 CGGGGAGCCGGCCACAGGGTCAGGC +s mm8.chrX 95535063 17 - 165556469 TATGGAAGAAGCCCCAA-------- + +a score=1368003.0 +s hg18.chrX 2219491 24 - 154913754 TTCTCCACCATGGTCTCTGTCCTG +s mm8.chrX 95535039 24 - 165556469 TTCTCTACCATGGTCTCCGTCCTG + diff -r e7b9d15e8e93 -r ff37fcf14bd5 tools/maf/interval2maf.py --- a/tools/maf/interval2maf.py Tue Sep 29 17:57:45 2009 -0400 +++ b/tools/maf/interval2maf.py Tue Sep 29 21:47:59 2009 -0400 @@ -80,6 +80,8 @@ split_blocks_by_species = True if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns': remove_all_gap_columns = True + else: + remove_all_gap_columns = True #Finish parsing command line #Open indexed access to MAFs @@ -113,6 +115,8 @@ for block in blocks: block = maf_utilities.chop_block_by_region( block, src, region ) if block is not None: + if species is not None: + block = block.limit_to_species( species ) block = maf_utilities.orient_block_by_region( block, src, region ) if remove_all_gap_columns: block.remove_all_gap_columns() diff -r e7b9d15e8e93 -r ff37fcf14bd5 tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Tue Sep 29 17:57:45 2009 -0400 +++ b/tools/maf/interval2maf.xml Tue Sep 29 21:47:59 2009 -0400 @@ -88,6 +88,14 @@ <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> <output name="out_file1" file="fsa_interval2maf.dat" /> </test> + <test> + <param name="input1" value="1.bed" dbkey="hg18" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="mafType" value="28_WAY_MULTIZ_hg18"/> + <param name="species" value="hg18,panTro2,mm8"/> + <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> + <output name="out_file1" file="interval2maf_3from28way.maf" /> + </test> </tests> <help> **What it does**

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