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

[hg] galaxy 1695: Add an option to override the output dataset(s...
by Nate Coraor 09 Jan '09

09 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/94df4d059b19 changeset: 1695:94df4d059b19 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jan 09 15:59:29 2009 -0500 description: Add an option to override the output dataset(s) path, so they may be written to the working directory. This allows administrators to mount datasets read-only on cluster nodes. 3 file(s) affected in this change: lib/galaxy/config.py lib/galaxy/jobs/__init__.py lib/galaxy/tools/__init__.py diffs (100 lines): diff -r 58744d4bda7b -r 94df4d059b19 lib/galaxy/config.py --- a/lib/galaxy/config.py Fri Jan 09 14:07:16 2009 -0500 +++ b/lib/galaxy/config.py Fri Jan 09 15:59:29 2009 -0500 @@ -45,6 +45,7 @@ self.job_scheduler_policy = kwargs.get("job_scheduler_policy", "FIFO") self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root ) + self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) ) self.admin_pass = kwargs.get('admin_pass',"galaxy") self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join(a)bx.psu.edu") diff -r 58744d4bda7b -r 94df4d059b19 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Jan 09 14:07:16 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Fri Jan 09 15:59:29 2009 -0500 @@ -350,7 +350,7 @@ incoming['userId'] = userId incoming['userEmail'] = userEmail # Build params, done before hook so hook can use - param_dict = self.tool.build_param_dict( incoming, inp_data, out_data ) + param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.working_directory ) # Certain tools require tasks to be completed prior to job execution # ( this used to be performed in the "exec_before_job" hook, but hooks are deprecated ). if self.tool.tool_type is not None: @@ -471,6 +471,13 @@ else: job.state = 'ok' for dataset_assoc in job.output_datasets: + if self.app.config.outputs_to_working_directory: + false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % dataset_assoc.dataset.id ) ) + if os.path.exists( false_path ): + os.rename( false_path, dataset_assoc.dataset.file_name ) + log.debug( "Moved %s to %s" % ( false_path, dataset_assoc.dataset.file_name ) ) + else: + log.warning( "Missing output file in working directory: %s" % false_path ) for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running dataset.blurb = 'done' dataset.peek = 'no peek' diff -r 58744d4bda7b -r 94df4d059b19 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Jan 09 14:07:16 2009 -0500 +++ b/lib/galaxy/tools/__init__.py Fri Jan 09 15:59:29 2009 -0500 @@ -1045,7 +1045,7 @@ input.validate( value, None ) input_values[ input.name ] = value - def build_param_dict( self, incoming, input_datasets, output_datasets ): + def build_param_dict( self, incoming, input_datasets, output_datasets, working_directory = None ): """ Build the dictionary of parameters for substituting into the command line. Each value is wrapped in a `InputValueWrapper`, which allows @@ -1090,7 +1090,13 @@ for child in data.children: param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) for name, data in output_datasets.items(): - param_dict[name] = DatasetFilenameWrapper( data ) + # Write outputs to the working directory (for security purposes) if desired. + if self.app.config.outputs_to_working_directory and working_directory is not None: + false_path = os.path.abspath( os.path.join( working_directory, "galaxy_dataset_%d.dat" % data.id ) ) + param_dict[name] = DatasetFilenameWrapper( data, false_path = false_path ) + open( false_path, 'w' ).close() + else: + param_dict[name] = DatasetFilenameWrapper( data ) # Provide access to a path to store additional files # TODO: path munging for cluster/dataset server relocatability param_dict[name].files_path = os.path.abspath(os.path.join(self.app.config.new_file_path, "dataset_%s_files" % (data.id) )) @@ -1433,7 +1439,7 @@ def items( self ): return iter( [ ( k, self.get( k ) ) for k, v in self.metadata.items() ] ) - def __init__( self, dataset, datatypes_registry = None, tool = None, name = None ): + def __init__( self, dataset, datatypes_registry = None, tool = None, name = None, false_path = None ): if not dataset: try: #TODO: allow this to work when working with grouping @@ -1444,10 +1450,17 @@ else: self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) + self.false_path = false_path def __str__( self ): - return self.dataset.file_name + if self.false_path is not None: + return self.false_path + else: + return self.dataset.file_name def __getattr__( self, key ): - return getattr( self.dataset, key ) + if self.false_path is not None and key == 'file_name': + return self.false_path + else: + return getattr( self.dataset, key ) def json_fix( val ): if isinstance( val, list ): @@ -1467,4 +1480,4 @@ value[composite_key] = incoming[key + "_" + composite_key] return value else: - return incoming.get( key, default ) \ No newline at end of file + return incoming.get( key, default )

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[hg] galaxy 1694: Allow upstream proxy to set wsgi.url_scheme, s...
by Nate Coraor 09 Jan '09

09 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/58744d4bda7b changeset: 1694:58744d4bda7b user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Jan 09 14:07:16 2009 -0500 description: Allow upstream proxy to set wsgi.url_scheme, so link generation is correct if the proxy uses a different transport with clients than it does with Galaxy. This doesn't work automatically. In Apache, you'd need to set the header yourself: RequestHeader set X-URL-SCHEME https For a discussion on how this affects links to the UCSC Genome Browser, see: http://mail.bx.psu.edu/pipermail/galaxy-user/2009-January/000430.html 2 file(s) affected in this change: lib/galaxy/web/framework/middleware/remoteuser.py lib/galaxy/web/framework/middleware/xforwardedhost.py diffs (25 lines): diff -r 4c1d1ce9265f -r 58744d4bda7b lib/galaxy/web/framework/middleware/remoteuser.py --- a/lib/galaxy/web/framework/middleware/remoteuser.py Thu Jan 08 11:04:19 2009 -0500 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Fri Jan 09 14:07:16 2009 -0500 @@ -62,6 +62,7 @@ # in the event of a lookup failure, deny access host = None if host in UCSC_SERVERS: + environ[ 'HTTP_REMOTE_USER' ] = 'ucsc_browser_display(a)example.org' return self.app( environ, start_response ) # Apache sets REMOTE_USER to the string '(null)' when using the # Rewrite* method for passing REMOTE_USER and a user is diff -r 4c1d1ce9265f -r 58744d4bda7b lib/galaxy/web/framework/middleware/xforwardedhost.py --- a/lib/galaxy/web/framework/middleware/xforwardedhost.py Thu Jan 08 11:04:19 2009 -0500 +++ b/lib/galaxy/web/framework/middleware/xforwardedhost.py Fri Jan 09 14:07:16 2009 -0500 @@ -14,4 +14,8 @@ if x_forwarded_for: environ[ 'ORGINAL_REMOTE_ADDR' ] = environ[ 'REMOTE_ADDR' ] environ[ 'REMOTE_ADDR' ] = x_forwarded_for - return self.app( environ, start_response ) \ No newline at end of file + x_url_scheme = environ.get( 'HTTP_X_URL_SCHEME', None ) + if x_url_scheme: + environ[ 'original_wsgi.url_scheme' ] = environ[ 'wsgi.url_scheme' ] + environ[ 'wsgi.url_scheme' ] = x_url_scheme + return self.app( environ, start_response )

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[hg] galaxy 1693: Fix from James Casbon for a problem he has exp...
by Nate Coraor 08 Jan '09

08 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4c1d1ce9265f changeset: 1693:4c1d1ce9265f user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Jan 08 11:04:19 2009 -0500 description: Fix from James Casbon for a problem he has experienced when using remote_user (a new user creation seems to be attempted before a session exists). 1 file(s) affected in this change: lib/galaxy/web/framework/__init__.py diffs (29 lines): diff -r 93b946a7d8cb -r 4c1d1ce9265f lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Wed Jan 07 15:33:35 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Thu Jan 08 11:04:19 2009 -0500 @@ -138,13 +138,22 @@ event.message = message % kwargs except: event.message = message - event.history = self.history + try: + event.history = self.history + except: + event.history = None try: event.history_id = self.history.id except: event.history_id = None - event.user = self.user - event.session_id = self.galaxy_session.id + try: + event.user = self.user + except: + event.user = None + try: + event.session_id = self.galaxy_session.id + except: + event.session_id = None event.flush() def get_cookie( self, name='galaxysession' ): """Convenience method for getting a session cookie"""

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[hg] galaxy 1692: Fix for my last commit.
by Greg Von Kuster 07 Jan '09

07 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/93b946a7d8cb changeset: 1692:93b946a7d8cb user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jan 07 15:33:35 2009 -0500 description: Fix for my last commit. 1 file(s) affected in this change: test/functional/test_sniffing_and_metadata_settings.py diffs (13 lines): diff -r 6e9dd26f782f -r 93b946a7d8cb test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Wed Jan 07 12:20:35 2009 -0500 +++ b/test/functional/test_sniffing_and_metadata_settings.py Wed Jan 07 15:33:35 2009 -0500 @@ -110,8 +110,7 @@ self.delete_history_item( 1 ) def test_60_blastxml_datatype( self ): """Testing correctly sniffing blastxml data type upon upload""" - self.upload_file( 'megablast_xml_parser_test1.blastxml' ) - self.verify_dataset_correctness( 'megablast_xml_parser_test1.blastxml' ) + self.upload_file( 'megablast_xml_parser_test1.gz' ) self.check_history_for_string( 'NCBI Blast XML data' ) self.check_history_for_string( 'format: <span class="blastxml">blastxml</span>' ) self.delete_history_item( 1 )

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[hg] galaxy 1691: Add support for NCBI Blast XML data format.
by Greg Von Kuster 07 Jan '09

07 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6e9dd26f782f changeset: 1691:6e9dd26f782f user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jan 07 12:20:35 2009 -0500 description: Add support for NCBI Blast XML data format. 8 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/registry.py lib/galaxy/datatypes/sniff.py lib/galaxy/datatypes/test/megablast_xml_parser_test1.blastxml lib/galaxy/datatypes/xml.py lib/galaxy/tools/actions/upload.py test/functional/test_sniffing_and_metadata_settings.py tools/metag_tools/megablast_xml_parser.xml diffs (truncated from 4398 to 3000 lines): diff -r 317d5f454dfd -r 6e9dd26f782f datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Tue Jan 06 13:29:03 2009 -0500 +++ b/datatypes_conf.xml.sample Wed Jan 07 12:20:35 2009 -0500 @@ -41,6 +41,7 @@ <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/> <datatype extension="txtseq.zip" type="galaxy.datatypes.images:Txtseq" mimetype="application/zip" display_in_upload="true"/> <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"/>  @@ -147,17 +148,18 @@ important because some formats are much more loosely defined than others. --> - <sniffer order="05" type="galaxy.datatypes.sequence:Maf"/> - <sniffer order="10" type="galaxy.datatypes.sequence:Lav"/> - <sniffer order="15" type="galaxy.datatypes.sequence:Fasta"/> - <sniffer order="25" type="galaxy.datatypes.sequence:FastqSolexa"/> - <sniffer order="30" type="galaxy.datatypes.interval:Wiggle"/> - <sniffer order="35" type="galaxy.datatypes.images:Html"/> - <sniffer order="40" type="galaxy.datatypes.sequence:Axt"/> - <sniffer order="45" type="galaxy.datatypes.interval:Bed"/> - <sniffer order="50" type="galaxy.datatypes.interval:CustomTrack"/> - <sniffer order="55" type="galaxy.datatypes.interval:Gff"/> - <sniffer order="60" type="galaxy.datatypes.interval:Gff3"/> - <sniffer order="65" type="galaxy.datatypes.interval:Interval"/> + <sniffer order="005" type="galaxy.datatypes.xml:BlastXml"/> + <sniffer order="010" type="galaxy.datatypes.sequence:Maf"/> + <sniffer order="015" type="galaxy.datatypes.sequence:Lav"/> + <sniffer order="020" type="galaxy.datatypes.sequence:Fasta"/> + <sniffer order="025" type="galaxy.datatypes.sequence:FastqSolexa"/> + <sniffer order="030" type="galaxy.datatypes.interval:Wiggle"/> + <sniffer order="035" type="galaxy.datatypes.images:Html"/> + <sniffer order="040" type="galaxy.datatypes.sequence:Axt"/> + <sniffer order="045" type="galaxy.datatypes.interval:Bed"/> + <sniffer order="050" type="galaxy.datatypes.interval:CustomTrack"/> + <sniffer order="055" type="galaxy.datatypes.interval:Gff"/> + <sniffer order="060" type="galaxy.datatypes.interval:Gff3"/> + <sniffer order="065" type="galaxy.datatypes.interval:Interval"/> </sniffers> </datatypes> diff -r 317d5f454dfd -r 6e9dd26f782f lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Tue Jan 06 13:29:03 2009 -0500 +++ b/lib/galaxy/datatypes/registry.py Wed Jan 07 12:20:35 2009 -0500 @@ -3,7 +3,7 @@ """ import os import logging -import data, tabular, interval, images, sequence, qualityscore, genetics +import data, tabular, interval, images, sequence, qualityscore, genetics, xml import galaxy.util from galaxy.util.odict import odict @@ -96,6 +96,7 @@ 'axt' : sequence.Axt(), 'bed' : interval.Bed(), 'binseq.zip' : images.Binseq(), + 'blastxml' : xml.BlastXml(), 'customtrack' : interval.CustomTrack(), 'csfasta' : sequence.csFasta(), 'fasta' : sequence.Fasta(), @@ -119,6 +120,7 @@ 'axt' : 'text/plain', 'bed' : 'text/plain', 'binseq.zip' : 'application/zip', + 'blastxml' : 'text/plain', 'customtrack' : 'text/plain', 'csfasta' : 'text/plain', 'fasta' : 'text/plain', @@ -141,6 +143,7 @@ # because some formats are much more flexibly defined than others. if len(self.sniff_order) < 1: self.sniff_order = [ + xml.BlastXml(), sequence.Maf(), sequence.Lav(), sequence.Fasta(), diff -r 317d5f454dfd -r 6e9dd26f782f lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Tue Jan 06 13:29:03 2009 -0500 +++ b/lib/galaxy/datatypes/sniff.py Wed Jan 07 12:20:35 2009 -0500 @@ -160,6 +160,9 @@ Returns an extension that can be used in the datatype factory to generate a data for the 'fname' file + >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml') + >>> guess_ext(fname) + 'blastxml' >>> fname = get_test_fname('interval.interval') >>> guess_ext(fname) 'interval' diff -r 317d5f454dfd -r 6e9dd26f782f lib/galaxy/datatypes/test/megablast_xml_parser_test1.blastxml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/megablast_xml_parser_test1.blastxml Wed Jan 07 12:20:35 2009 -0500 @@ -0,0 +1,4117 @@ +<?xml version="1.0"?> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> +<BlastOutput> + <BlastOutput_program>blastn</BlastOutput_program> + <BlastOutput_version>blastn 2.2.17 [Aug-26-2007]</BlastOutput_version> + <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> + <BlastOutput_db>Ecoli.fa</BlastOutput_db> + <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID> + <BlastOutput_query-def>0_0.666667</BlastOutput_query-def> + <BlastOutput_query-len>30</BlastOutput_query-len> + <BlastOutput_param> + <Parameters> + <Parameters_expect>10</Parameters_expect> + <Parameters_sc-match>1</Parameters_sc-match> + <Parameters_sc-mismatch>-3</Parameters_sc-mismatch> + <Parameters_gap-open>0</Parameters_gap-open> + <Parameters_gap-extend>0</Parameters_gap-extend> + <Parameters_filter>F</Parameters_filter> + </Parameters> + </BlastOutput_param> + <BlastOutput_iterations> + <Iteration> + <Iteration_iter-num>1</Iteration_iter-num> + <Iteration_query-ID>lcl|1_0</Iteration_query-ID> + <Iteration_query-def>0_0.666667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>5436010</Hsp_hit-from> + <Hsp_hit-to>5436039</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGGACAGCGCCGCCACCAACAAAGCCACCA</Hsp_qseq> + <Hsp_hseq>CGGACAGCGCCGCCACCAACAAAGCCACCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>2</Iteration_iter-num> + <Iteration_query-ID>lcl|2_0</Iteration_query-ID> + <Iteration_query-def>1_0.600000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>696993</Hsp_hit-from> + <Hsp_hit-to>697022</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAAACACCGGATGCTCCGGCGCTGGCAGAT</Hsp_qseq> + <Hsp_hseq>AAAACACCGGATGCTCCGGCGCTGGCAGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>3</Iteration_iter-num> + <Iteration_query-ID>lcl|3_0</Iteration_query-ID> + <Iteration_query-def>2_0.400000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4100018</Hsp_hit-from> + <Hsp_hit-to>4100047</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTTGCTTTTAGTACACCGGATTCAGAACCA</Hsp_qseq> + <Hsp_hseq>TTTGCTTTTAGTACACCGGATTCAGAACCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>4</Iteration_iter-num> + <Iteration_query-ID>lcl|4_0</Iteration_query-ID> + <Iteration_query-def>3_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> 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<Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4626492</Hsp_hit-from> + <Hsp_hit-to>4626521</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACCCCGATATCGTCGCAGGCGTTGCCGCAC</Hsp_qseq> + <Hsp_hseq>ACCCCGATATCGTCGCAGGCGTTGCCGCAC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>16</Iteration_iter-num> + <Iteration_query-ID>lcl|16_0</Iteration_query-ID> + <Iteration_query-def>15_0.666667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>346897</Hsp_hit-from> + <Hsp_hit-to>346926</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1466536</Hsp_hit-from> + <Hsp_hit-to>1466565</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GAAGCGCCTCTTCCAGCGGAGACAGCAGCC</Hsp_qseq> + <Hsp_hseq>GAAGCGCCTCTTCCAGCGGAGACAGCAGCC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1750132</Hsp_hit-from> + <Hsp_hit-to>1750161</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1908046</Hsp_hit-from> + <Hsp_hit-to>1908075</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2279107</Hsp_hit-from> + <Hsp_hit-to>2279136</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>6</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2813407</Hsp_hit-from> + <Hsp_hit-to>2813436</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>7</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3939162</Hsp_hit-from> + <Hsp_hit-to>3939191</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>8</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4656510</Hsp_hit-from> + <Hsp_hit-to>4656539</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_qseq> + <Hsp_hseq>GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>17</Iteration_iter-num> + <Iteration_query-ID>lcl|17_0</Iteration_query-ID> + <Iteration_query-def>16_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2595157</Hsp_hit-from> + <Hsp_hit-to>2595186</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ATGTCCTGATCGAGCGGCGTTTTACCGACC</Hsp_qseq> + <Hsp_hseq>ATGTCCTGATCGAGCGGCGTTTTACCGACC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>18</Iteration_iter-num> + <Iteration_query-ID>lcl|18_0</Iteration_query-ID> + <Iteration_query-def>17_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>717743</Hsp_hit-from> + <Hsp_hit-to>717772</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGTGTTGAGTGTCCAGGTAATACGCTCTCG</Hsp_qseq> + <Hsp_hseq>GGTGTTGAGTGTCCAGGTAATACGCTCTCG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>20</Iteration_iter-num> + <Iteration_query-ID>lcl|20_0</Iteration_query-ID> + <Iteration_query-def>19_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1237938</Hsp_hit-from> + <Hsp_hit-to>1237967</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GTTGTAAGCGTCAGAACCGATGCGGTCGGT</Hsp_qseq> + <Hsp_hseq>GTTGTAAGCGTCAGAACCGATGCGGTCGGT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>21</Iteration_iter-num> + <Iteration_query-ID>lcl|21_0</Iteration_query-ID> + <Iteration_query-def>20_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + 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<Iteration_query-def>21_0.733333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>269757</Hsp_hit-from> + <Hsp_hit-to>269786</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GGGAAGGCTGACGGGCGTCCACACCACGGC</Hsp_qseq> + <Hsp_hseq>GGGAAGGCTGACGGGCGTCCACACCACGGC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + 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<Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>23</Iteration_iter-num> + <Iteration_query-ID>lcl|23_0</Iteration_query-ID> + <Iteration_query-def>22_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2706426</Hsp_hit-from> + <Hsp_hit-to>2706455</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + 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<Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1512107</Hsp_hit-from> + <Hsp_hit-to>1512136</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTGCCGTTACGCACCACGCCTTCAGTAGCG</Hsp_qseq> + <Hsp_hseq>TTGCCGTTACGCACCACGCCTTCAGTAGCG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + 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</Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>29</Iteration_iter-num> + <Iteration_query-ID>lcl|29_0</Iteration_query-ID> + <Iteration_query-def>28_0.666667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4405442</Hsp_hit-from> + <Hsp_hit-to>4405471</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + 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</Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>35</Iteration_iter-num> + <Iteration_query-ID>lcl|35_0</Iteration_query-ID> + <Iteration_query-def>34_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>484499</Hsp_hit-from> + <Hsp_hit-to>484528</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGATGTTAAATGCATGGCACCTGCCGGTGC</Hsp_qseq> + <Hsp_hseq>TGATGTTAAATGCATGGCACCTGCCGGTGC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>36</Iteration_iter-num> + <Iteration_query-ID>lcl|36_0</Iteration_query-ID> + <Iteration_query-def>35_0.466667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2250064</Hsp_hit-from> + <Hsp_hit-to>2250093</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACTGCTTTGCCGAGATATTCGAGGTTAACC</Hsp_qseq> + <Hsp_hseq>ACTGCTTTGCCGAGATATTCGAGGTTAACC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>37</Iteration_iter-num> + <Iteration_query-ID>lcl|37_0</Iteration_query-ID> + <Iteration_query-def>36_0.433333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3698178</Hsp_hit-from> + <Hsp_hit-to>3698207</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGTTGGCAACATGGCGAGCGTAATCAATTA</Hsp_qseq> + <Hsp_hseq>TGTTGGCAACATGGCGAGCGTAATCAATTA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>39</Iteration_iter-num> + <Iteration_query-ID>lcl|39_0</Iteration_query-ID> + <Iteration_query-def>38_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4242501</Hsp_hit-from> + <Hsp_hit-to>4242530</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GCAGCAGGATCGGATCGAACTCTGGTTTCT</Hsp_qseq> + <Hsp_hseq>GCAGCAGGATCGGATCGAACTCTGGTTTCT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>40</Iteration_iter-num> + <Iteration_query-ID>lcl|40_0</Iteration_query-ID> + <Iteration_query-def>39_0.400000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3683151</Hsp_hit-from> + <Hsp_hit-to>3683180</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TAATGCGGCATTCTCCTGATTTATTGTCAC</Hsp_qseq> + <Hsp_hseq>TAATGCGGCATTCTCCTGATTTATTGTCAC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>42</Iteration_iter-num> + <Iteration_query-ID>lcl|42_0</Iteration_query-ID> + <Iteration_query-def>41_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>789086</Hsp_hit-from> + <Hsp_hit-to>789115</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AGCTGACGGTCAGCAGGGATACTTCCTGCA</Hsp_qseq> + <Hsp_hseq>AGCTGACGGTCAGCAGGGATACTTCCTGCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>43</Iteration_iter-num> + <Iteration_query-ID>lcl|43_0</Iteration_query-ID> + <Iteration_query-def>42_0.566667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1714771</Hsp_hit-from> + <Hsp_hit-to>1714800</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GCAGTGACTACATCCGCGAGGTGAATGTGG</Hsp_qseq> + <Hsp_hseq>GCAGTGACTACATCCGCGAGGTGAATGTGG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>44</Iteration_iter-num> + <Iteration_query-ID>lcl|44_0</Iteration_query-ID> + <Iteration_query-def>43_0.466667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4272582</Hsp_hit-from> + <Hsp_hit-to>4272611</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GCTTTTTCCAGCATCAACGCCACTGAACAA</Hsp_qseq> + <Hsp_hseq>GCTTTTTCCAGCATCAACGCCACTGAACAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>45</Iteration_iter-num> + <Iteration_query-ID>lcl|45_0</Iteration_query-ID> + <Iteration_query-def>44_0.433333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>5481023</Hsp_hit-from> + <Hsp_hit-to>5481052</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>AAAGTGGTAGATAACGTGGTGCAGACTATG</Hsp_qseq> + <Hsp_hseq>AAAGTGGTAGATAACGTGGTGCAGACTATG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>46</Iteration_iter-num> + <Iteration_query-ID>lcl|46_0</Iteration_query-ID> + <Iteration_query-def>45_0.500000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1271829</Hsp_hit-from> + <Hsp_hit-to>1271858</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ATCCGCGATAAGGTCATCCGGTATCAGGAA</Hsp_qseq> + <Hsp_hseq>ATCCGCGATAAGGTCATCCGGTATCAGGAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>1357952</Hsp_hit-from> + <Hsp_hit-to>1357981</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ATCCGCGATAAGGTCATCCGGTATCAGGAA</Hsp_qseq> + <Hsp_hseq>ATCCGCGATAAGGTCATCCGGTATCAGGAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2310674</Hsp_hit-from> + <Hsp_hit-to>2310703</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_qseq> + <Hsp_hseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2769319</Hsp_hit-from> + <Hsp_hit-to>2769348</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_qseq> + <Hsp_hseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2991293</Hsp_hit-from> + <Hsp_hit-to>2991322</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_qseq> + <Hsp_hseq>TTCCTGATACCGGATGACCTTATCGCGGAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>47</Iteration_iter-num> + <Iteration_query-ID>lcl|47_0</Iteration_query-ID> + <Iteration_query-def>46_0.466667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1080570</Hsp_hit-from> + <Hsp_hit-to>1080599</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_qseq> + <Hsp_hseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1476177</Hsp_hit-from> + <Hsp_hit-to>1476206</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_qseq> + <Hsp_hseq>ACCTGTACCCCAGGACCATGGTACATTTAT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>48</Iteration_iter-num> + <Iteration_query-ID>lcl|48_0</Iteration_query-ID> + <Iteration_query-def>47_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>2887871</Hsp_hit-from> + <Hsp_hit-to>2887900</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ACAATGCAACCAGACCAGCCCGGATCGATA</Hsp_qseq> + <Hsp_hseq>ACAATGCAACCAGACCAGCCCGGATCGATA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>50</Iteration_iter-num> + <Iteration_query-ID>lcl|50_0</Iteration_query-ID> + <Iteration_query-def>49_0.433333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>4152853</Hsp_hit-from> + <Hsp_hit-to>4152882</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGTTATACGGAACAACATTTAACTCCAGCG</Hsp_qseq> + <Hsp_hseq>CGTTATACGGAACAACATTTAACTCCAGCG</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>51</Iteration_iter-num> + <Iteration_query-ID>lcl|51_0</Iteration_query-ID> + <Iteration_query-def>50_0.466667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3568677</Hsp_hit-from> + <Hsp_hit-to>3568706</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TTGCTGTTGCCATCGCTTTTCAGGACATAC</Hsp_qseq> + <Hsp_hseq>TTGCTGTTGCCATCGCTTTTCAGGACATAC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>52</Iteration_iter-num> + <Iteration_query-ID>lcl|52_0</Iteration_query-ID> + <Iteration_query-def>51_0.533333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3739788</Hsp_hit-from> + <Hsp_hit-to>3739817</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>CGACGGTATCGGTACGCAGATTGTGATGGA</Hsp_qseq> + <Hsp_hseq>CGACGGTATCGGTACGCAGATTGTGATGGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>53</Iteration_iter-num> + <Iteration_query-ID>lcl|53_0</Iteration_query-ID> + <Iteration_query-def>52_0.366667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3789407</Hsp_hit-from> + <Hsp_hit-to>3789436</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>ATGAGCATCAACATCGAAATCTCAAACCAA</Hsp_qseq> + <Hsp_hseq>ATGAGCATCAACATCGAAATCTCAAACCAA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>55</Iteration_iter-num> + <Iteration_query-ID>lcl|55_0</Iteration_query-ID> + <Iteration_query-def>54_0.400000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>3161991</Hsp_hit-from> + <Hsp_hit-to>3162020</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GTATTCTTCATTGATTTGTAAGCGGGTACC</Hsp_qseq> + <Hsp_hseq>GTATTCTTCATTGATTTGTAAGCGGGTACC</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>56</Iteration_iter-num> + <Iteration_query-ID>lcl|56_0</Iteration_query-ID> + 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</Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>57</Iteration_iter-num> + <Iteration_query-ID>lcl|57_0</Iteration_query-ID> + <Iteration_query-def>56_0.433333</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + 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<Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>62</Iteration_iter-num> + <Iteration_query-ID>lcl|62_0</Iteration_query-ID> + <Iteration_query-def>61_0.366667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1987157</Hsp_hit-from> + <Hsp_hit-to>1987186</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT</Hsp_qseq> + <Hsp_hseq>TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>63</Iteration_iter-num> + <Iteration_query-ID>lcl|63_0</Iteration_query-ID> + <Iteration_query-def>62_0.366667</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>1667830</Hsp_hit-from> + <Hsp_hit-to>1667859</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + 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<Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>231418</Hsp_hit-from> + <Hsp_hit-to>231447</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + 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<Hsp_hseq>TCACGCTCGCAGTCAAGCTGGCTTATGCCA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>4808457</Hsp_hit-from> + <Hsp_hit-to>4808486</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>4904735</Hsp_hit-from> + <Hsp_hit-to>4904764</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>6</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>5048915</Hsp_hit-from> + <Hsp_hit-to>5048944</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>7</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>30</Hsp_query-from> + <Hsp_query-to>1</Hsp_query-to> + <Hsp_hit-from>5089922</Hsp_hit-from> + <Hsp_hit-to>5089951</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>-1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_qseq> + <Hsp_hseq>TGGCATAAGCCAGCTTGACTGCGAGCGTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> + </Hit> + </Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>1</Statistics_db-num> + <Statistics_db-len>5528445</Statistics_db-len> + <Statistics_hsp-len>0</Statistics_hsp-len> + <Statistics_eff-space>0</Statistics_eff-space> + <Statistics_kappa>0.711</Statistics_kappa> + <Statistics_lambda>1.374</Statistics_lambda> + <Statistics_entropy>1.31</Statistics_entropy> + </Statistics> + </Iteration_stat> + </Iteration> + <Iteration> + <Iteration_iter-num>65</Iteration_iter-num> + <Iteration_query-ID>lcl|65_0</Iteration_query-ID> + <Iteration_query-def>64_0.500000</Iteration_query-def> + <Iteration_query-len>30</Iteration_query-len> + <Iteration_hits> + <Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|0</Hit_id> + <Hit_def>/depot/data2/galaxy/microbes/eschColi_O157H7EDL933_1/seq/chr.nib:1-5528445</Hit_def> + <Hit_accession>0</Hit_accession> + <Hit_len>5528445</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>59.96</Hsp_bit-score> + <Hsp_score>30</Hsp_score> + <Hsp_evalue>8.38112e-11</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>30</Hsp_query-to> + <Hsp_hit-from>5440369</Hsp_hit-from> + <Hsp_hit-to>5440398</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>30</Hsp_identity> + <Hsp_positive>30</Hsp_positive> + <Hsp_align-len>30</Hsp_align-len> + <Hsp_qseq>GAGATGACGGTTGCAGAGTCATGCGTTTGA</Hsp_qseq> + <Hsp_hseq>GAGATGACGGTTGCAGAGTCATGCGTTTGA</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps>

1 0

[hg] galaxy 1690: log exceptions when removing temporary files w...
by Greg Von Kuster 06 Jan '09

06 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/317d5f454dfd changeset: 1690:317d5f454dfd user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 06 13:29:03 2009 -0500 description: log exceptions when removing temporary files when upload fails. 1 file(s) affected in this change: lib/galaxy/tools/actions/upload.py diffs (30 lines): diff -r cf3c6da6f552 -r 317d5f454dfd lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Tue Jan 06 11:35:49 2009 -0500 +++ b/lib/galaxy/tools/actions/upload.py Tue Jan 06 13:29:03 2009 -0500 @@ -63,7 +63,7 @@ # Attempt to remove temporary file os.unlink( temp_name ) except: - pass + log.exception( 'failure removing temporary file: %s' % temp_name ) errmsg = 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) return self.upload_empty( trans, job, "Error:", errmsg ) try: @@ -84,7 +84,7 @@ # Attempt to remove temporary file os.unlink( temp_name ) except: - pass + log.exception( 'failure removing temporary file: %s' % temp_name ) errmsg = 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) return self.upload_empty( trans, job, "Error:", errmsg ) try: @@ -107,7 +107,7 @@ # Attempt to remove temporary file os.unlink( temp_name ) except: - pass + log.exception( 'failure removing temporary file: %s' % temp_name ) errmsg = 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) return self.upload_empty( trans, job, "Error:", errmsg ) try:

1 0

[hg] galaxy 1689: Better exception handling, messaging for uploa...
by Greg Von Kuster 06 Jan '09

06 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cf3c6da6f552 changeset: 1689:cf3c6da6f552 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 06 11:35:49 2009 -0500 description: Better exception handling, messaging for upload utility. 3 file(s) affected in this change: lib/galaxy/datatypes/sniff.py lib/galaxy/tools/actions/upload.py test/functional/test_toolbox.py diffs (140 lines): diff -r e0162b7bf0ba -r cf3c6da6f552 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py Tue Jan 06 11:11:24 2009 -0500 +++ b/lib/galaxy/datatypes/sniff.py Tue Jan 06 11:35:49 2009 -0500 @@ -12,11 +12,11 @@ full_path = os.path.join(path, 'test', fname) return full_path -def stream_to_file(stream): +def stream_to_file( stream, suffix='', prefix='', dir=None, text=False ): """ Writes a stream to a temporary file, returns the temporary file's name """ - fd, temp_name = tempfile.mkstemp() + fd, temp_name = tempfile.mkstemp( suffix=suffix, prefix=prefix, dir=dir, text=text ) while 1: chunk = stream.read(1048576) if not chunk: diff -r e0162b7bf0ba -r cf3c6da6f552 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Tue Jan 06 11:11:24 2009 -0500 +++ b/lib/galaxy/tools/actions/upload.py Tue Jan 06 11:35:49 2009 -0500 @@ -44,22 +44,33 @@ trans.log_event( 'created job id %d' % job.id, tool_id=tool.id ) if 'local_filename' in dir( data_file ): # Use the existing file + file_name = data_file.filename + file_name = file_name.split( '\\' )[-1] + file_name = file_name.split( '/' )[-1] try: - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using datafile.local_filename %s: %s' % ( data_file.local_filename, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) elif 'filename' in dir( data_file ): + file_name = data_file.filename + file_name = file_name.split( '\\' )[-1] + file_name = file_name.split( '/' )[-1] try: - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] - temp_name = sniff.stream_to_file( data_file.file ) + temp_name = sniff.stream_to_file( data_file.file, prefix='upload' ) + except Exception, e: + try: + # Attempt to remove temporary file + os.unlink( temp_name ) + except: + pass + errmsg = 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) + try: data_list.append( self.add_file( trans, temp_name, file_name, file_type, dbkey, space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using file temp_name %s: %s' % ( str( temp_name ), str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) if url_paste not in [ None, "" ]: if url_paste.lower().find( 'http://' ) >= 0 or url_paste.lower().find( 'ftp://' ) >= 0: url_paste = url_paste.replace( '\r', '' ).split( '\n' ) @@ -67,10 +78,20 @@ line = line.rstrip( '\r\n' ) if line: try: - temp_name = sniff.stream_to_file( urllib.urlopen( line ) ) + temp_name = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) + except Exception, e: + try: + # Attempt to remove temporary file + os.unlink( temp_name ) + except: + pass + errmsg = 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) + try: data_list.append( self.add_file( trans, temp_name, line, file_type, dbkey, info="uploaded url", space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using url_paste temp_name %s: %s' % ( str( temp_name ), str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) else: is_valid = False for line in url_paste: @@ -80,10 +101,20 @@ break if is_valid: try: - temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ) ) + temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) + except Exception, e: + try: + # Attempt to remove temporary file + os.unlink( temp_name ) + except: + pass + errmsg = 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) + try: data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, dbkey, info="pasted entry", space_to_tab=space_to_tab ) ) except Exception, e: - return self.upload_empty( trans, job, "Error:", str( e ) ) + errmsg = 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) + return self.upload_empty( trans, job, "Error:", errmsg ) else: return self.upload_empty( trans, job, "No data error:", "you pasted no data." ) if self.empty: @@ -103,7 +134,7 @@ log.info("End of tool %s execution for job id %d, memory used increased by %s" % ( tool.id, job.id, m1 ) ) return dict( output=hda ) - def upload_empty(self, trans, job, err_code, err_msg): + def upload_empty( self, trans, job, err_code, err_msg ): data = trans.app.model.HistoryDatasetAssociation( create_dataset = True ) data.name = err_code data.extension = "txt" @@ -119,8 +150,8 @@ job.info = err_msg job.add_output_dataset( data.name, data ) job.flush() - log.info( 'job id %d ended with errors' % job.id ) - trans.log_event( 'job id %d ended with errors' % job.id, tool_id=job.tool_id ) + log.info( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ) ) + trans.log_event( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ), tool_id=job.tool_id ) return dict( output=data ) def add_file( self, trans, temp_name, file_name, file_type, dbkey, info=None, space_to_tab=False ): diff -r e0162b7bf0ba -r cf3c6da6f552 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Tue Jan 06 11:11:24 2009 -0500 +++ b/test/functional/test_toolbox.py Tue Jan 06 11:35:49 2009 -0500 @@ -8,7 +8,6 @@ class ToolTestCase( TwillTestCase ): """Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`""" def do_it( self ): - print "###self.testdef: ", self.testdef # If the test generation had an error, raise if self.testdef.error: if self.testdef.exception:

1 0

[hg] galaxy 1688: Added a new option to the grouping tool to fac...
by Greg Von Kuster 06 Jan '09

06 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e0162b7bf0ba changeset: 1688:e0162b7bf0ba user: guru date: Tue Jan 06 11:11:24 2009 -0500 description: Added a new option to the grouping tool to facilitate picking of random entries from columns not chosen for either grouping or aggregate operations. 2 file(s) affected in this change: tools/stats/grouping.py tools/stats/grouping.xml diffs (230 lines): diff -r 091573fd6e27 -r e0162b7bf0ba tools/stats/grouping.py --- a/tools/stats/grouping.py Mon Jan 05 15:26:17 2009 -0500 +++ b/tools/stats/grouping.py Tue Jan 06 11:11:24 2009 -0500 @@ -12,13 +12,15 @@ def main(): inputfile = sys.argv[2] + in_columns = int( sys.argv[5] ) + show_remaining_cols = sys.argv[4] ops = [] cols = [] rounds = [] elems = [] - for var in sys.argv[4:]: + for var in sys.argv[6:]: ops.append(var.split()[0]) cols.append(var.split()[1]) rounds.append(var.split()[2]) @@ -79,9 +81,19 @@ if error_code != 0: stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout )) - + + if show_remaining_cols == 'yes': + show_cols_list = [1]*in_columns + show_cols_list[group_col] = 0 + for c in cols: + c = int(c)-1 + show_cols_list[c] = 0 + #at the end of this, only the indices of the remaining columns will be set to 1 + remaining_cols = [j for j,k in enumerate(show_cols_list) if k==1] #this is the list of remaining column indices + prev_item = "" prev_vals = [] + remaining_vals = [] skipped_lines = 0 first_invalid_line = 0 invalid_line = '' @@ -116,22 +128,30 @@ invalid_column = col+1 if valid: prev_vals[i].append(fields[col].strip()) + #Store values from all the remaning columns + if show_remaining_cols == 'yes': + for j, index in enumerate(remaining_cols): + remaining_vals[j].append(fields[index].strip()) else: """ When a new value is encountered, write the previous value and the corresponding aggregate values into the output file. This works due to the sort on group_col we've applied to the data above. """ - out_str = prev_item - + out_list = ['']*in_columns + out_list[group_col] = str(prev_item) + for i, op in enumerate( ops ): rfunc = "r." + op if op not in ['c','length','unique','random']: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) - rout = "%g" %( eval( rfunc )( prev_vals[i] )) if rounds[i] == 'yes': + rout = "%f" %( eval( rfunc )( prev_vals[i] )) rout = int(round(float(rout))) + else: + rout = "%g" %( eval( rfunc )( prev_vals[i] )) + else: if op != 'random': rout = eval( rfunc )( prev_vals[i] ) @@ -142,9 +162,21 @@ if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) - out_str += "\t" + str(rout) - - print >>fout, out_str + + out_list[int(cols[i])-1] = str(rout) + + if show_remaining_cols == 'yes': + for index,el in enumerate(remaining_cols): + if index == 0: + try: + random_index = random.randint(0,len(remaining_vals[index])-1) + except: + random_index = 0 + #pick a random value from each of the remaning columns + rand_out = remaining_vals[index][random_index] + out_list[el] = str(rand_out) + + print >>fout, '\t'.join([elem for elem in out_list if elem != '']) prev_item = item prev_vals = [] @@ -153,6 +185,14 @@ val_list = [] val_list.append(fields[col].strip()) prev_vals.append(val_list) + + if show_remaining_cols == 'yes': + remaining_vals = [] + for index in remaining_cols: + remaining_val_list = [] + remaining_val_list.append(fields[index].strip()) + remaining_vals.append(remaining_val_list) + else: # This only occurs once, right at the start of the iteration. prev_item = item @@ -161,8 +201,15 @@ val_list = [] val_list.append(fields[col].strip()) prev_vals.append(val_list) + + if show_remaining_cols == 'yes': + remaining_vals = [] + for index in remaining_cols: + remaining_val_list = [] + remaining_val_list.append(fields[index].strip()) + remaining_vals.append(remaining_val_list) - except Exception, exc: + except Exception: skipped_lines += 1 if not first_invalid_line: first_invalid_line = ii+1 @@ -172,7 +219,8 @@ first_invalid_line = ii+1 # Handle the last grouped value - out_str = prev_item + out_list = ['']*in_columns + out_list[group_col] = str(prev_item) for i, op in enumerate(ops): rfunc = "r." + op @@ -180,9 +228,11 @@ if op not in ['c','length','unique','random']: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) - rout = '%g' %( eval( rfunc )( prev_vals[i] )) if rounds[i] == 'yes': + rout = '%f' %( eval( rfunc )( prev_vals[i] )) rout = int(round(float(rout))) + else: + rout = '%g' %( eval( rfunc )( prev_vals[i] )) else: if op != 'random': rout = eval( rfunc )( prev_vals[i] ) @@ -193,13 +243,22 @@ if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) - out_str += "\t" + str( rout ) + out_list[int(cols[i])-1] = str(rout) except: skipped_lines += 1 if not first_invalid_line: first_invalid_line = ii+1 + if show_remaining_cols == 'yes': + for index,el in enumerate(remaining_cols): + if index == 0: + try: + random_index = random.randint(0,len(remaining_vals[index])-1) + except: + random_index = 0 + rand_out = remaining_vals[index][random_index] + out_list[el] = str(rand_out) - print >>fout, out_str + print >>fout, '\t'.join([elem for elem in out_list if elem != '']) # Generate a useful info message. msg = "--Group by c%d: " %(group_col+1) diff -r 091573fd6e27 -r e0162b7bf0ba tools/stats/grouping.xml --- a/tools/stats/grouping.xml Mon Jan 05 15:26:17 2009 -0500 +++ b/tools/stats/grouping.xml Tue Jan 06 11:11:24 2009 -0500 @@ -1,10 +1,12 @@ -<tool id="Grouping1" name="Group" version="1.4.0"> +<tool id="Grouping1" name="Group" version="1.5.0"> <description>data by a column and perform aggregate operation on other columns.</description> <command interpreter="python"> grouping.py $out_file1 $input1 - $groupcol + $groupcol + $othercols + ${input1.metadata.columns} #for $op in $operations '${op.optype} ${op.opcol} @@ -30,7 +32,11 @@ <option value="no">NO</option> <option value="yes">YES</option> </param> - </repeat> + </repeat> + <param name="othercols" type="select" label="Randomly pick an entry from each of the remaining columns (besides the columns chosen for group and aggregate operations above) ?"> + <option value="no">NO</option> + <option value="yes">YES</option> + </param> </inputs> <outputs> <data format="input" name="out_file1" metadata_source="input1" /> @@ -46,9 +52,9 @@ <param name="optype" value="mean"/> <param name="opcol" value="2"/> <param name="opround" value="no"/> + <param name="othercols" value="no"/> <output name="out_file1" file="groupby_out1.dat"/> </test> -  <test> <param name="input1" value="1.tabular"/> @@ -56,6 +62,7 @@ <param name="optype" value="mean"/> <param name="opcol" value="2"/> <param name="opround" value="no"/> + <param name="othercols" value="no"/> <output name="out_file1" file="groupby_out2.dat"/> </test> </tests>

1 0

[hg] galaxy 1687: megablast fix from Anton
by Nate Coraor 05 Jan '09

05 Jan '09

details: http://www.bx.psu.edu/hg/galaxy/rev/091573fd6e27 changeset: 1687:091573fd6e27 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Jan 05 15:26:17 2009 -0500 description: megablast fix from Anton 1 file(s) affected in this change: tools/metag_tools/megablast_xml_parser.py diffs (20 lines): diff -r 696fc4c02a0c -r 091573fd6e27 tools/metag_tools/megablast_xml_parser.py --- a/tools/metag_tools/megablast_xml_parser.py Tue Dec 23 13:28:27 2008 -0500 +++ b/tools/metag_tools/megablast_xml_parser.py Mon Jan 05 15:26:17 2009 -0500 @@ -1,6 +1,6 @@ #! /usr/bin/python -import sys, os +import sys, os, re assert sys.version_info[:2] >= ( 2, 4 ) @@ -55,6 +55,8 @@ # for every <Hit> within <Iteration> for hit in elem.findall( "Iteration_hits/Hit/" ): subject = hit.findtext( "Hit_id" ) + if re.search( '^gi', subject ): + subject = subject.split('|')[1] sLen = hit.findtext( "Hit_len" ) # for every <Hsp> within <Hit> for hsp in hit.findall( "Hit_hsps/Hsp" ):

1 0