details: http://www.bx.psu.edu/hg/galaxy/rev/93b8b571a9fa changeset: 2767:93b8b571a9fa user: Kanwei Li <kanwei@gmail.com> date: Thu Sep 24 16:16:56 2009 -0400 description: merge 0 file(s) affected in this change: diffs (595 lines): diff -r 9e0c6e9b9dbb -r 93b8b571a9fa lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu Sep 24 16:15:57 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Thu Sep 24 16:16:56 2009 -0400 @@ -48,9 +48,6 @@ # FIXME: hardcoding this for now, but it should be derived from the available # converters browsable_types = set( ["wig" ] ) - -# For natural sort -NUM_RE = re.compile('([0-9]+)') class TracksController( BaseController ): """ @@ -122,8 +119,14 @@ """ Returns a naturally sorted list of chroms/contigs for the given dbkey """ + def check_int(s): + if s.isdigit(): + return int(s) + else: + return s + def split_by_number(s): - return [ int(c) if c.isdigit() else c for c in NUM_RE.split(s) ] + return [ check_int(c) for c in re.split('([0-9]+)', s) ] chroms = self._chroms( trans, dbkey ) to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()] diff -r 9e0c6e9b9dbb -r 93b8b571a9fa scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Thu Sep 24 16:15:57 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Thu Sep 24 16:16:56 2009 -0400 @@ -204,32 +204,42 @@ def delete_datasets( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ): # Marks datasets as deleted if associated items are all deleted. - print '# The following datasets have been marked deleted' + print "######### Starting delete_datasets #########\n" start = time.clock() if force_retry: - datasets = app.model.Dataset.filter( app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time ).all() + app.model.Dataset.filter( app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time ).all() - else: - datasets = app.model.Dataset.filter( and_( app.model.HistoryDatasetAssociation.table.c.deleted==True, - app.model.Dataset.table.c.deleted == False, - app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time ) ).all() - datasets = datasets + app.model.Dataset.filter( and_( app.model.LibraryDatasetDatasetAssociation.table.c.deleted==True, - app.model.Dataset.table.c.deleted == False, - app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time ) ).all() + history_datasets = app.model.Dataset.options( eagerload( "history_associations" ) ) \ + .filter( app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time ).all() + library_datasets = app.model.Dataset.options( eagerload( "library_associations" ) ) \ + .filter( app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time ).all() + else: + history_datasets = app.model.Dataset.filter_by( deleted = False ) \ + .options( eagerload( "history_associations" ) ) \ + .filter( and_( app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time, + app.model.HistoryDatasetAssociation.table.c.deleted==True ) ).all() + library_datasets = app.model.Dataset.filter_by( deleted = False ) \ + .options( eagerload( "library_associations" ) ) \ + .filter( and_( app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time, + app.model.LibraryDatasetDatasetAssociation.table.c.deleted==True ) ).all() + print "Time to query history and library datasets: ", time.clock() - start, "\n" + print "Processing ", len( history_datasets ), " history datasets and ", len( library_datasets ), " library datasets...\n\n" + datasets = history_datasets + library_datasets skip = [] deleted_dataset_count = 0 deleted_instance_count = 0 for dataset in datasets: + print "Processing dataset id:", dataset.id, "\n" if dataset.id not in skip and _dataset_is_deletable( dataset ): deleted_dataset_count += 1 - print "Dataset:", dataset.id for dataset_instance in dataset.history_associations + dataset.library_associations: - print "\tAssociated Dataset instance:", dataset_instance.__class__.__name__, dataset_instance.id - _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children = True, info_only = info_only ) + print "Associated Dataset instance: ", dataset_instance.__class__.__name__, dataset_instance.id, "\n" + _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True ) deleted_instance_count += 1 skip.append( dataset.id ) - print - print '# Examined %d datasets, marked %d as deleted and purged %d dataset instances\n' % ( len( skip ), deleted_dataset_count, deleted_instance_count ) - print "Elapsed time: ", time.clock() - start, "\n" + print "Time to process dataset id: ", dataset.id, " - ", time.clock() - start, "\n\n" + print "Time to mark datasets deleted: ", time.clock() - start, "\n\n" + print "Examined %d datasets, marked %d as deleted and purged %d dataset instances\n" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) + print "Total elapsed time: ", time.clock() - start, "\n" + print "######### Finished delete_datasets #########\n" def purge_datasets( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ): # Purges deleted datasets whose update_time is older than cutoff_time. Files may or may @@ -262,15 +272,16 @@ print "Elapsed time: ", stop - start, "\n" -def _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children = True, info_only = False ): - #purging a dataset instance marks the instance as deleted, - #and marks the dataset as deleted if it is not associated with another DatsetInstance that is not deleted +def _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=False, is_deletable=False ): + # A dataset_instance is either a HDA or an LDDA. Purging a dataset instance marks the instance as deleted, + # and marks the associated dataset as deleted if it is not associated with another active DatsetInstance. if not info_only: dataset_instance.mark_deleted( include_children = include_children ) dataset_instance.clear_associated_files() dataset_instance.flush() dataset_instance.dataset.refresh() - if _dataset_is_deletable( dataset_instance.dataset ): + if is_deletable or _dataset_is_deletable( dataset_instance.dataset ): + # Calling methods may have already checked _dataset_is_deletable, if so, is_deletable should be True _delete_dataset( dataset_instance.dataset, app, remove_from_disk, info_only = info_only ) #need to purge children here if include_children: diff -r 9e0c6e9b9dbb -r 93b8b571a9fa templates/root/history.mako --- a/templates/root/history.mako Thu Sep 24 16:15:57 2009 -0400 +++ b/templates/root/history.mako Thu Sep 24 16:16:56 2009 -0400 @@ -81,7 +81,7 @@ // Functionized so AJAX'd datasets can call them function initShowHide() { - // Load saved state and show as neccesary + // Load saved state and show as necessary try { var stored = $.jStore.store("history_expand_state"); if (stored) { diff -r 9e0c6e9b9dbb -r 93b8b571a9fa test-data/cat_wrapper_out1.bed --- a/test-data/cat_wrapper_out1.bed Thu Sep 24 16:15:57 2009 -0400 +++ b/test-data/cat_wrapper_out1.bed Thu Sep 24 16:16:56 2009 -0400 @@ -131,28 +131,3 @@ chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - -chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, -chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, -chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, -chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, -chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, -chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, -chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, -chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, -chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, -chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, -chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, -chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, -chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, -chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, -chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, -chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, -chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, -chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, -chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, -chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, -chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, -chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, -chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, -chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, -chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, diff -r 9e0c6e9b9dbb -r 93b8b571a9fa tools/filters/catWrapper.py --- a/tools/filters/catWrapper.py Thu Sep 24 16:15:57 2009 -0400 +++ b/tools/filters/catWrapper.py Thu Sep 24 16:16:56 2009 -0400 @@ -11,19 +11,28 @@ def main(): outfile = sys.argv[1] infile = sys.argv[2] - catfiles = sys.argv[3:] + try: fout = open(sys.argv[1],'w') - except Exxception, ex: - stop_err("Output file cannot be opened for writing\n" + str(ex)) + except: + stop_err("Output file cannot be opened for writing.") + try: fin = open(sys.argv[2],'r') - except Exception, ex: - stop_err("Input file cannot be opened for reading\n" + str(ex)) - cmdline = "cat %s %s > %s" % (infile, ' '.join(catfiles), outfile) + except: + stop_err("Input file cannot be opened for reading.") + + if len(sys.argv) < 4: + os.system("cp %s %s" %(infile,outfile)) + sys.exit() + + cmdline = "cat %s " %(infile) + for inp in sys.argv[3:]: + cmdline = cmdline + inp + " " + cmdline = cmdline + ">" + outfile try: os.system(cmdline) - except Exception, ex: - stop_err("Error encountered with cat\n" + str(ex)) + except: + stop_err("Error encountered with cat.") if __name__ == "__main__": main() \ No newline at end of file diff -r 9e0c6e9b9dbb -r 93b8b571a9fa tools/filters/catWrapper.xml --- a/tools/filters/catWrapper.xml Thu Sep 24 16:15:57 2009 -0400 +++ b/tools/filters/catWrapper.xml Thu Sep 24 16:16:56 2009 -0400 @@ -1,19 +1,17 @@ -<tool id="cat1" name="Concatenate queries" version="1.0.1"> +<tool id="cat1" name="Concatenate queries"> <description>tail-to-head</description> - <command interpreter="python"> - catWrapper.py - $out_file1 + <command interpreter="python"> + catWrapper.py + $out_file1 $input1 - $input2 - #for $q in $queries - ${q.input3} - #end for + #for $q in $queries + ${q.input2} + #end for </command> <inputs> - <param name="input1" type="data" label="First query to concatenate:"/> - <param name="input2" type="data" label="Second query to concatenate:"/> - <repeat name="queries" title="Additional query"> - <param name="input3" type="data" label="Select" /> + <param name="input1" type="data" label="Concatenate Query"/> + <repeat name="queries" title="Query"> + <param name="input2" type="data" label="Select" /> </repeat> </inputs> <outputs> @@ -23,16 +21,14 @@ <test> <param name="input1" value="1.bed"/> <param name="input2" value="2.bed"/> - <param name="input3" value="3.bed"/> <output name="out_file1" file="cat_wrapper_out1.bed"/> </test> <!--TODO: if possible, enhance the underlying test code to handle this test - the problem is multiple params with the same name "input3" + the problem is multiple params with the same name "input2" <test> <param name="input1" value="1.bed"/> <param name="input2" value="2.bed"/> - <param name="input3" value="3.bed"/> - <param name="input3" value="4.bed"/> + <param name="input2" value="3.bed"/> <output name="out_file1" file="cat_wrapper_out2.bed"/> </test> --> @@ -62,12 +58,12 @@ chr1 151242630 151242955 X 0 + chr1 151271715 151271999 Y 0 + - chr1 151278832 151279227 Z 0 - - -and with Query2:: - - chr2 100000030 200000955 P 0 + - chr2 100000015 200000999 Q 0 + + chr1 151278832 151279227 Z 0 - + +and with Query2:: + + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + will result in the following:: @@ -76,8 +72,8 @@ chr1 151242630 151242955 X 0 + chr1 151271715 151271999 Y 0 + chr1 151278832 151279227 Z 0 - - chr2 100000030 200000955 P 0 + - chr2 100000015 200000999 Q 0 + + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + </help> </tool> diff -r 9e0c6e9b9dbb -r 93b8b571a9fa tools/filters/sorter.py --- a/tools/filters/sorter.py Thu Sep 24 16:15:57 2009 -0400 +++ b/tools/filters/sorter.py Thu Sep 24 16:16:56 2009 -0400 @@ -1,28 +1,44 @@ -# This script sorts a file based on the inputs: -# -cols - column to sort on -# -order - ASC- or DESCending order -# -i - input filename -# -o - output filename +""" +Sorts tabular data on one or more columns. + +usage: %prog [options] + -i, --input=i: Tabular file to be sorted + -o, --out_file1=o: Sorted output file + -c, --column=c: First column to sort on + -s, --style=s: Sort style (numerical or alphabetical) + -r, --order=r: Order (ASC or DESC) + +usage: %prog input out_file1 column style order [column style ...] +""" import os, re, string, sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) sys.exit() def main(): + #Parse Command Line + options, args = doc_optparse.parse( __doc__ ) try: - inputfile = sys.argv[1] - outputfile = '-o %s' % sys.argv[2] - order = ('', '-r')[sys.argv[3] == 'DESC'] - sort_type = ('','-n')[sys.argv[4] == 'num'] - columns = sys.argv[5:] - cols = [ '-k%s,%s'%(n, n) for n in columns ] + inputfile = options.input + outputfile = '-o %s' % options.out_file1 + order = ('', '-r')[options.order == 'DESC'] + columns = [options.column] + styles = [('','n')[options.style == 'num']] + col_styles = sys.argv[6:] + if len(col_styles) > 1: + columns.extend([col_styles[i] for i in range(0,len(col_styles),2)]) + styles.extend([('','n')[col_styles[i] == 'num'] for i in range(1,len(col_styles),2)]) + cols = [ '-k%s,%s%s'%(columns[i], columns[i], styles[i]) for i in range(len(columns)) ] except Exception, ex: stop_err('Error parsing input parameters\n' + str(ex)) # Launch sort. - cmd = "sort -f -t $'\t' %s %s %s %s %s" % (sort_type, ' '.join(cols), order, outputfile, inputfile) + cmd = "sort -f -t $'\t' %s %s %s %s" % (order, ' '.join(cols), outputfile, inputfile) try: os.system(cmd) except Exception, ex: diff -r 9e0c6e9b9dbb -r 93b8b571a9fa tools/filters/sorter.xml --- a/tools/filters/sorter.xml Thu Sep 24 16:15:57 2009 -0400 +++ b/tools/filters/sorter.xml Thu Sep 24 16:16:56 2009 -0400 @@ -2,28 +2,33 @@ <description>data in ascending or descending order</description> <command interpreter="python"> sorter.py - $input - $out_file1 - $order - $style - $firstcol + --input=$input + --out_file1=$out_file1 + --column=$column + --style=$style + --order=$order #for $col in $column_set: - ${col.column} + ${col.other_column} + ${col.other_style} #end for </command> <inputs> <param format="tabular" name="input" type="data" label="Sort Query" /> - <param name="firstcol" label="on column" type="data_column" data_ref="input" accept_default="true" /> - <repeat name="column_set" title="Column selection"> - <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> - </repeat> - <param name="order" type="select" label="in"> - <option value="DESC">Descending order</option> - <option value="ASC">Ascending order</option> - </param> + <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> <param name="style" type="select" label="with flavor"> <option value="num">Numerical sort</option> <option value="alpha">Alphabetical sort</option> + </param> + <repeat name="column_set" title="Column selection"> + <param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" /> + <param name="other_style" type="select" label="with flavor"> + <option value="num">Numerical sort</option> + <option value="alpha">Alphabetical sort</option> + </param> + </repeat> + <param name="order" type="select" label="everything in"> + <option value="DESC">Descending order</option> + <option value="ASC">Ascending order</option> </param> </inputs> <outputs> @@ -32,18 +37,20 @@ <tests> <test> <param name="input" value="sort_in1.bed"/> - <param name="firstcol" value="1"/> - <param name="column" value="3" /> + <param name="column" value="1"/> + <param name="style" value="num"/> + <param name="other_column" value="3"/> + <param name="other_style" value="num"/> <param name="order" value="ASC"/> - <param name="style" value="num"/> <output name="out_file1" file="sort_out1.bed"/> </test> <test> <param name="input" value="sort_in1.bed"/> - <param name="firstcol" value="3" /> - <param name="column" value="1"/> + <param name="column" value="3"/> + <param name="style" value="alpha"/> + <param name="other_column" value="1"/> + <param name="other_style" value="alpha"/> <param name="order" value="ASC"/> - <param name="style" value="alpha"/> <output name="out_file1" file="sort_out2.bed"/> </test> </tests> @@ -64,9 +71,53 @@ ----- -**Example** +**Examples** The list of numbers 4,17,3,5 collates to 3,4,5,17 by numerical sorting, while it collates to 17,3,4,5 by alphabetical sorting. +Sorting the following:: + + Q d 7 II jhu 45 + A kk 4 I h 111 + Pd p 1 ktY WS 113 + A g 10 H ZZ 856 + A edf 4 tw b 234 + BBB rt 10 H ZZ 100 + A rew 10 d b 1111 + C sd 19 YH aa 10 + Hah c 23 ver bb 467 + MN gtr 1 a X 32 + N j 9 a T 205 + BBB rrf 10 b Z 134 + odfr ws 6 Weg dew 201 + C f 3 WW SW 34 + A jhg 4 I b 345 + Pd gf 7 Gthe de 567 + rS hty 90 YY LOp 89 + A g 10 H h 43 + A g 4 I h 500 + +on columns 1 (alpha), 3 (num), and 6 (num) in ascending order will yield:: + + A kk 4 I h 111 + A edf 4 tw b 234 + A jhg 4 I b 345 + A g 4 I h 500 + A g 10 H h 43 + A g 10 H ZZ 856 + A rew 10 d b 1111 + BBB rt 10 H ZZ 100 + BBB rrf 10 b Z 134 + C f 3 WW SW 34 + C sd 19 YH aa 10 + Hah c 23 ver bb 467 + MN gtr 1 a X 32 + N j 9 a T 205 + odfr ws 6 Weg dew 201 + Pd p 1 ktY WS 113 + Pd gf 7 Gthe de 567 + Q d 7 II jhu 45 + rS hty 90 YY LOp 89 + </help> </tool> diff -r 9e0c6e9b9dbb -r 93b8b571a9fa tools/next_gen_conversion/solid_to_fastq.py --- a/tools/next_gen_conversion/solid_to_fastq.py Thu Sep 24 16:15:57 2009 -0400 +++ b/tools/next_gen_conversion/solid_to_fastq.py Thu Sep 24 16:16:56 2009 -0400 @@ -30,7 +30,7 @@ tmpf = tempfile.NamedTemporaryFile() #forward reads if options.input3 != "None" and options.input4 != "None": tmpr = tempfile.NamedTemporaryFile() #reverse reads - cmd1 = "bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4) + cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(os.path.split(sys.argv[0])[0], tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4) try: os.system(cmd1) os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1)) @@ -40,7 +40,7 @@ tmpr.close() # if single-end data else: - cmd1 = "bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (tmpf.name, None, None, options.input1, options.input2, None, None) + cmd1 = "%s/bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (os.path.split(sys.argv[0])[0], tmpf.name, None, None, options.input1, options.input2, None, None) try: os.system(cmd1) os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1)) diff -r 9e0c6e9b9dbb -r 93b8b571a9fa tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Thu Sep 24 16:15:57 2009 -0400 +++ b/tools/samtools/sam_pileup.xml Thu Sep 24 16:16:56 2009 -0400 @@ -56,13 +56,13 @@ </param> <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" /> <conditional name="c"> - <param name="consensus" type="select" label="Whether or not to call the consensus sequence using the MAQ consensus model"> - <option value="no">Don't use MAQ consensus model</option> - <option value="yes">Use the MAQ consensus model</option> + <param name="consensus" type="select" label="Call consensus according to MAQ model?"> + <option selected="true" value="no">No</option> + <option value="yes">Yes</option> </param> <when value="no" /> <when value="yes"> - <param name="theta" type="float" value="0.85" label="Theta paramter (error dependency coefficient) in the MAQ consensus calling model" /> + <param name="theta" type="float" value="0.85" label="Theta parameter (error dependency coefficient) in the MAQ consensus calling model" /> <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" /> <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" /> <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" /> @@ -77,9 +77,68 @@ **What it does** -Uses SAMTools_' pileup command to produce a file in the pileup format based on the provided BAM file. +Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generated two types of pileup datasets depending on chosen options. If *Call consensus according to MAQ model?* option is set to **No**, the tool produces simple pileup. If the option is set to **Yes**, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + +------ + +**Types of pileup datasets** + +The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below. + +.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml + +**Six column pileup**:: + + 1 2 3 4 5 6 + --------------------------------- + chrM 412 A 2 ., II + chrM 413 G 4 ..t, IIIH + chrM 414 C 4 ...a III2 + chrM 415 C 4 TTTt III7 + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Coverage (# reads aligning over that position) + 5 Bases within reads where (see Galaxy wiki for more info) + 6 Quality values (phred33 scale, see Galaxy wiki for more) + +**Ten column pileup** + +The `ten-column`__ pileup incoroporates additional consensus information generated with *-c* option of *samtools pileup* command:: + + + 1 2 3 4 5 6 7 8 9 10 + ------------------------------------------------ + chrM 412 A A 75 0 25 2 ., II + chrM 413 G G 72 0 25 4 ..t, IIIH + chrM 414 C C 75 0 25 4 ...a III2 + chrM 415 C T 75 75 25 4 TTTt III7 + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Consensus bases + 5 Consensus quality + 6 SNP quality + 7 Maximum mapping quality + 8 Coverage (# reads aligning over that position) + 9 Bases within reads where (see Galaxy wiki for more info) + 10 Quality values (phred33 scale, see Galaxy wiki for more) + + +.. __: http://samtools.sourceforge.net/cns0.shtml + </help> </tool> diff -r 9e0c6e9b9dbb -r 93b8b571a9fa tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Thu Sep 24 16:15:57 2009 -0400 +++ b/tools/samtools/sam_to_bam.xml Thu Sep 24 16:16:56 2009 -0400 @@ -51,7 +51,7 @@ **What it does** -This tool uses the SAMTools_ toolkit to produce a BAM file based on a sorted input SAM file. +This tool uses the SAMTools_ toolkit to produce a indexed BAM file based on a sorted input SAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml