| Previous changeset 2:376ed15e0d27 (2017-03-24) Next changeset 4:363f3480622d (2017-10-12) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty |
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modified:
blast_parser.xml test-data/output.tabular |
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added:
blast_parser.py test-data/output2.tabular |
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removed:
blast_parser.pl |
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| diff -r 376ed15e0d27 -r 70df762b48a8 blast_parser.pl --- a/blast_parser.pl Fri Mar 24 12:14:47 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,43 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; -use List::Util qw(min max); - -# A simple Perl parser to convert a BLAST 12-column or 24-column output into a -# 3-column input for hcluster_hg (id1, id2, weight): -# parse_blast.pl <file> - -use constant LOG_E_10 => log(10); - -my $file1 = $ARGV[0]; -open my $fh1, '<', $file1; - -while (my $line = <$fh1>) { - my @row = split(/\t/, $line); - - if ($row[0] eq $row[1]) { - # ignore self matching hits - } else { - # Convert evalue to an integer weight with max 100 - my $weight = 100; - - #if the evalue is 0, leave weight at 100 - if ($row[10] != 0 && $row[10] != 0.0) { - $weight = min(100, positive_round(-1 * log10($row[10]))); - } - print"$row[0]\t$row[1]\t$weight\n"; - } -} -close $fh1; - -# Calculate logarithm to base 10 of a number -sub log10 { - my $n = shift; - return log($n) / LOG_E_10; -} - -# Round a positive float to the nearest integer -sub positive_round{ - my $n = shift; - return int($n + 0.5); -} |
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| diff -r 376ed15e0d27 -r 70df762b48a8 blast_parser.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast_parser.py Tue Oct 03 04:51:45 2017 -0400 |
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| @@ -0,0 +1,54 @@ +""" +Simple parser to convert a BLAST 12-column or 24-column tabular output into a +3-column tabular input for hcluster_hg (id1, id2, weight): +""" +import argparse +import math +from collections import OrderedDict + + +def main(): + parser = argparse.ArgumentParser() + + parser.add_argument('-i', metavar='in-file', type=argparse.FileType('rt'), required=True, help='Path to input file') + + parser.add_argument('-o', metavar='out-file', type=argparse.FileType('wt'), required=True, help='Path to output file') + + parser.add_argument('-r', action='store_true', default=False, + dest='reciprocal', + help='Annotate homolog pair') + + parser.add_argument('--version', action='version', version='%(prog)s 1.0') + + options = parser.parse_args() + + results = OrderedDict() + + for line in options.i: + line = line.rstrip() + line_cols = line.split('\t') + sequence1_id = line_cols[0] + sequence2_id = line_cols[1] + evalue = float(line_cols[10]) + + # Ignore self-matching hits + if sequence1_id != sequence2_id: + # Convert evalue to an integer weight with max 100 + weight = 100 + + # If the evalue is 0, leave weight at 100 + if evalue != 0.0: + weight = min(100, round(math.log10(evalue) / -2.0)) + + if (sequence1_id, sequence2_id) not in results: + results[(sequence1_id, sequence2_id)] = weight + else: + results[(sequence1_id, sequence2_id)] = max(results[(sequence1_id, sequence2_id)], weight) + + for (sequence1_id, sequence2_id), weight in results.items(): + if not options.reciprocal or (sequence2_id, sequence1_id) in results: + options.o.write("%s\t%s\t%d\n" % (sequence1_id, sequence2_id, weight)) + + +if __name__ == "__main__": + main() |
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| diff -r 376ed15e0d27 -r 70df762b48a8 blast_parser.xml --- a/blast_parser.xml Fri Mar 24 12:14:47 2017 -0400 +++ b/blast_parser.xml Tue Oct 03 04:51:45 2017 -0400 |
| [ |
| @@ -1,18 +1,22 @@ -<tool id="blast_parser" name="BLAST parser" version="0.1.1"> +<tool id="blast_parser" name="BLAST parser" version="0.1.2"> <description> Convert 12- or 24-column BLAST output into 3-column hcluster_sg input </description> <command detect_errors="exit_code"> <![CDATA[ -perl '$__tool_directory__/blast_parser.pl' -'$input' -> '$output' +python '$__tool_directory__/blast_parser.py' +-i '$input' +-o '$output' +#if $reciprocal + -r +#end if ]]> </command> <inputs> <param name="input" type="data" format="tabular" label="Tabular data" help="BLAST 12 column tabular format data"/> + <param name="reciprocal" type="boolean" checked="false" label="Reciprocal results" help="returns only reciprocal results"/> </inputs> <outputs> @@ -22,12 +26,18 @@ <tests> <test> <param name="input" ftype="tabular" value="input.tabular" /> + <param name="reciprocal" value="false" /> <output name="output" file="output.tabular" /> </test> + <test> + <param name="input" ftype="tabular" value="input.tabular" /> + <param name="reciprocal" value="true" /> + <output name="output" file="output2.tabular" /> + </test> </tests> <help> <![CDATA[ -Simple tool to convert a 12- or 24-column BLAST output into a 3-column format (qseqid, sseqid, round(-1 * log10(evalue))) usable as input for the hcluster_sg tool. +Simple tool to convert a 12- or 24-column BLAST output into a 3-column format (qseqid, sseqid, round(-1 * log10(evalue)/2)) usable as input for the hcluster_sg tool. ]]> </help> <citations> |
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| diff -r 376ed15e0d27 -r 70df762b48a8 test-data/output.tabular --- a/test-data/output.tabular Fri Mar 24 12:14:47 2017 -0400 +++ b/test-data/output.tabular Tue Oct 03 04:51:45 2017 -0400 |
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| @@ -4,24 +4,22 @@ ENSPCAT00000008534_procaviacapensis_1 ENST00000378069_homosapiens_1 100 ENSLOCT00000017020_lepisosteusoculatus_1 ENSLACT00000026689_latimeriachalumnae_1 100 ENSCPOT00000000986_caviaporcellus_1 ENSCAFT00000022963_canisfamiliaris_1 100 -ENSTGUT00000016508_taeniopygiaguttata_1 ENSTGUT00000006603_taeniopygiaguttata_1 100 +ENSTGUT00000016508_taeniopygiaguttata_1 ENSTGUT00000006603_taeniopygiaguttata_1 79 ENSPFOT00000010657_poeciliaformosa_1 ENSXMAT00000001796_xiphophorusmaculatus_1 100 ENSDNOT00000016434_dasypusnovemcinctus_1 ENSDNOT00000036768_dasypusnovemcinctus_1 100 -ENSPMAT00000010398_petromyzonmarinus_1 ENSLACT00000015911_latimeriachalumnae_1 64 +ENSPMAT00000010398_petromyzonmarinus_1 ENSLACT00000015911_latimeriachalumnae_1 32 ENSAMET00000018099_ailuropodamelanoleuca_1 ENSCAFT00000022939_canisfamiliaris_1 100 ENSEEUT00000005606_erinaceuseuropaeus_1 ENSMPUT00000012759_mustelaputoriusfuro_1 100 ENSSHAT00000006757_sarcophilusharrisii_1 ENSMODT00000026841_monodelphisdomestica_1 100 ENSPSIT00000017454_pelodiscussinensis_1 ENSPSIT00000017443_pelodiscussinensis_1 100 ENSPFOT00000022544_poeciliaformosa_1 ENSXMAT00000001796_xiphophorusmaculatus_1 100 ENSMICT00000002052_microcebusmurinus_1 ENSCAFT00000022963_canisfamiliaris_1 100 -ENSMICT00000002052_microcebusmurinus_1 ENSCAFT00000022963_canisfamiliaris_1 46 ENSRNOT00000066674_rattusnorvegicus_1 ENSMUST00000026013_musmusculus_1 100 ENSFCAT00000013090_feliscatus_1 ENSAMET00000018029_ailuropodamelanoleuca_1 100 ENSONIT00000020514_oreochromisniloticus_1 ENSPFOT00000009022_poeciliaformosa_1 100 ENSLACT00000026572_latimeriachalumnae_1 ENSLACT00000015911_latimeriachalumnae_1 100 -ENSPMAT00000003449_petromyzonmarinus_1 ENSGGOT00000000206_gorillagorilla_1 100 +ENSPMAT00000003449_petromyzonmarinus_1 ENSGGOT00000000206_gorillagorilla_1 75 ENSSART00000014230_sorexaraneus_1 ENSSTOT00000004965_ictidomystridecemlineatus_1 100 -ENSSART00000014230_sorexaraneus_1 ENSSTOT00000004965_ictidomystridecemlineatus_1 44 ENSBTAT00000001698_bostaurus_1 ENSCAFT00000022963_canisfamiliaris_1 100 ENSTBET00000006983_tupaiabelangeri_1 ENSAMET00000018099_ailuropodamelanoleuca_1 100 ENSLACT00000014274_latimeriachalumnae_1 ENSLACT00000026689_latimeriachalumnae_1 100 @@ -38,8 +36,7 @@ ENSXMAT00000001796_xiphophorusmaculatus_1 ENSONIT00000016435_oreochromisniloticus_1 100 ENSSSCT00000013404_susscrofa_1 ENSPPYT00000023637_pongoabelii_1 100 ENSGALT00000036672_gallusgallus_1 ENSMGAT00000016429_meleagrisgallopavo_1 100 -ENSOPRT00000017156_ochotonaprinceps_1 ENSOCUT00000001438_oryctolaguscuniculus_1 100 -ENSOPRT00000017156_ochotonaprinceps_1 ENSOCUT00000001438_oryctolaguscuniculus_1 17 +ENSOPRT00000017156_ochotonaprinceps_1 ENSOCUT00000001438_oryctolaguscuniculus_1 70 ENSSTOT00000004988_ictidomystridecemlineatus_1 ENSPANT00000027606_papioanubis_1 100 ENSECAT00000024641_equuscaballus_1 ENSCAFT00000022939_canisfamiliaris_1 100 ENSAPLT00000013855_anasplatyrhynchos_1 ENSMGAT00000016431_meleagrisgallopavo_1 100 @@ -48,7 +45,7 @@ ENSPTRT00000040521_pantroglodytes_1 ENSGGOT00000000206_gorillagorilla_1 100 ENSPTRT00000040520_pantroglodytes_1 ENSPPYT00000023637_pongoabelii_1 100 ENSMEUT00000003745_macropuseugenii_1 ENSMODT00000026841_monodelphisdomestica_1 100 -ENSMICT00000002042_microcebusmurinus_1 ENSDNOT00000039756_dasypusnovemcinctus_1 100 +ENSMICT00000002042_microcebusmurinus_1 ENSDNOT00000039756_dasypusnovemcinctus_1 85 ENSXETT00000010517_xenopustropicalis_1 ENSXETT00000010521_xenopustropicalis_1 100 ENSMODT00000026840_monodelphisdomestica_1 ENSCAFT00000022963_canisfamiliaris_1 100 ENSMLUT00000001428_myotislucifugus_1 ENSAMET00000018099_ailuropodamelanoleuca_1 100 @@ -59,8 +56,8 @@ ENSTRUT00000035430_takifugurubripes_1 ENSTNIT00000014720_tetraodonnigroviridis_1 100 ENSMEUT00000006183_macropuseugenii_1 ENSMODT00000026840_monodelphisdomestica_1 100 ENSFALT00000001591_ficedulaalbicollis_1 ENSTGUT00000006603_taeniopygiaguttata_1 100 -ENSMUST00000168613_musmusculus_1 ENSMUST00000040820_musmusculus_1 100 -ENSSSCT00000032764_susscrofa_1 ENSSSCT00000013404_susscrofa_1 100 +ENSMUST00000168613_musmusculus_1 ENSMUST00000040820_musmusculus_1 76 +ENSSSCT00000032764_susscrofa_1 ENSSSCT00000013404_susscrofa_1 53 ENSGALT00000026158_gallusgallus_1 ENSMGAT00000016431_meleagrisgallopavo_1 100 ENSDART00000160057_daniorerio_1 ENSDART00000132084_daniorerio_1 100 ENSMPUT00000012759_mustelaputoriusfuro_1 ENSCAFT00000022939_canisfamiliaris_1 100 @@ -92,11 +89,10 @@ ENSSTOT00000004965_ictidomystridecemlineatus_1 ENSECAT00000024641_equuscaballus_1 100 ENSMLUT00000001440_myotislucifugus_1 ENSPANT00000027606_papioanubis_1 100 ENSORLT00000017214_oryziaslatipes_1 ENSPFOT00000009022_poeciliaformosa_1 100 -ENSMUST00000163344_musmusculus_1 ENSMUST00000168613_musmusculus_1 63 +ENSMUST00000163344_musmusculus_1 ENSMUST00000168613_musmusculus_1 31 ENSACAT00000017993_anoliscarolinensis_1 ENSPSIT00000017443_pelodiscussinensis_1 100 ENSCJAT00000021080_callithrixjacchus_1 ENSCJAT00000058575_callithrixjacchus_1 100 -ENSOPRT00000000678_ochotonaprinceps_1 ENSOGAT00000030491_otolemurgarnettii_1 100 -ENSOPRT00000000678_ochotonaprinceps_1 ENSOGAT00000030491_otolemurgarnettii_1 19 +ENSOPRT00000000678_ochotonaprinceps_1 ENSOGAT00000030491_otolemurgarnettii_1 71 ENSMMUT00000027384_macacamulatta_1 ENSPANT00000027701_papioanubis_1 100 ENSMMUT00000027387_macacamulatta_1 ENSPANT00000027631_papioanubis_1 100 ENSLOCT00000019886_lepisosteusoculatus_1 ENSDART00000160057_daniorerio_1 100 @@ -118,7 +114,7 @@ ENSTTRT00000009129_tursiopstruncatus_1 ENSCAFT00000022963_canisfamiliaris_1 100 ENSCAFT00000022963_canisfamiliaris_1 ENSAMET00000018029_ailuropodamelanoleuca_1 100 ENSGGOT00000008973_gorillagorilla_1 ENSPPYT00000023637_pongoabelii_1 100 -ENSOGAT00000031973_otolemurgarnettii_1 ENSOGAT00000005620_otolemurgarnettii_1 100 +ENSOGAT00000031973_otolemurgarnettii_1 ENSOGAT00000005620_otolemurgarnettii_1 77 ENSGACT00000024065_gasterosteusaculeatus_1 ENSGACT00000024064_gasterosteusaculeatus_1 100 ENSGACT00000024064_gasterosteusaculeatus_1 ENSGACT00000024065_gasterosteusaculeatus_1 100 ENSAMET00000018029_ailuropodamelanoleuca_1 ENSCAFT00000022963_canisfamiliaris_1 100 @@ -142,19 +138,19 @@ ENSLAFT00000027936_loxodontaafricana_1 ENSLAFT00000015029_loxodontaafricana_1 100 ENSPSIT00000016442_pelodiscussinensis_1 ENSAPLT00000013117_anasplatyrhynchos_1 100 ENSOART00000003319_ovisaries_1 ENSBTAT00000021570_bostaurus_1 100 -ENSMMUT00000046681_macacamulatta_1 ENSPANT00000027701_papioanubis_1 28 -ENSMMUT00000046680_macacamulatta_1 ENSCSAT00000012035_chlorocebussabaeus_1 44 +ENSMMUT00000046681_macacamulatta_1 ENSPANT00000027701_papioanubis_1 14 +ENSMMUT00000046680_macacamulatta_1 ENSCSAT00000012035_chlorocebussabaeus_1 22 ENSBTAT00000021570_bostaurus_1 ENSOART00000003319_ovisaries_1 100 ENST00000378069_homosapiens_1 ENSGGOT00000000206_gorillagorilla_1 100 ENSPANT00000027606_papioanubis_1 ENSPANT00000027631_papioanubis_1 100 ENSLAFT00000000504_loxodontaafricana_1 ENSECAT00000024641_equuscaballus_1 100 ENSPCAT00000006605_procaviacapensis_1 ENSLAFT00000000504_loxodontaafricana_1 100 ENSLOCT00000002323_lepisosteusoculatus_1 ENSDART00000028225_daniorerio_1 100 -ENSMUST00000173143_musmusculus_1 ENSMUST00000163344_musmusculus_1 5 +ENSMUST00000173143_musmusculus_1 ENSMUST00000163344_musmusculus_1 3 ENSRNOT00000044009_rattusnorvegicus_1 ENSMUST00000040820_musmusculus_1 100 ENSMODT00000026841_monodelphisdomestica_1 ENSCAFT00000022939_canisfamiliaris_1 100 ENSLACT00000015911_latimeriachalumnae_1 ENSLACT00000026572_latimeriachalumnae_1 100 -ENSSSCT00000035258_susscrofa_1 ENSSSCT00000013404_susscrofa_1 97 +ENSSSCT00000035258_susscrofa_1 ENSSSCT00000013404_susscrofa_1 48 ENSTRUT00000011582_takifugurubripes_1 ENSTRUT00000011581_takifugurubripes_1 100 ENSPSIT00000017443_pelodiscussinensis_1 ENSPSIT00000017454_pelodiscussinensis_1 100 ENSTRUT00000011580_takifugurubripes_1 ENSTRUT00000011581_takifugurubripes_1 100 |
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| diff -r 376ed15e0d27 -r 70df762b48a8 test-data/output2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.tabular Tue Oct 03 04:51:45 2017 -0400 |
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| @@ -0,0 +1,50 @@ +ENSFCAT00000013089_feliscatus_1 ENSCAFT00000022939_canisfamiliaris_1 100 +ENSCAFT00000022939_canisfamiliaris_1 ENSFCAT00000013089_feliscatus_1 100 +ENSAMXT00000002585_astyanaxmexicanus_1 ENSDART00000028225_daniorerio_1 100 +ENSPSIT00000017454_pelodiscussinensis_1 ENSPSIT00000017443_pelodiscussinensis_1 100 +ENSRNOT00000066674_rattusnorvegicus_1 ENSMUST00000026013_musmusculus_1 100 +ENSLACT00000026572_latimeriachalumnae_1 ENSLACT00000015911_latimeriachalumnae_1 100 +ENSTGUT00000006603_taeniopygiaguttata_1 ENSFALT00000001591_ficedulaalbicollis_1 100 +ENSFALT00000001560_ficedulaalbicollis_1 ENSTGUT00000006498_taeniopygiaguttata_1 100 +ENSXMAT00000001796_xiphophorusmaculatus_1 ENSONIT00000016435_oreochromisniloticus_1 100 +ENSGALT00000036672_gallusgallus_1 ENSMGAT00000016429_meleagrisgallopavo_1 100 +ENSAPLT00000013855_anasplatyrhynchos_1 ENSMGAT00000016431_meleagrisgallopavo_1 100 +ENSDART00000132084_daniorerio_1 ENSDART00000160057_daniorerio_1 100 +ENSPTRT00000040521_pantroglodytes_1 ENSGGOT00000000206_gorillagorilla_1 100 +ENSXETT00000010517_xenopustropicalis_1 ENSXETT00000010521_xenopustropicalis_1 100 +ENSTRUT00000035430_takifugurubripes_1 ENSTNIT00000014720_tetraodonnigroviridis_1 100 +ENSFALT00000001591_ficedulaalbicollis_1 ENSTGUT00000006603_taeniopygiaguttata_1 100 +ENSDART00000160057_daniorerio_1 ENSDART00000132084_daniorerio_1 100 +ENSLACT00000014695_latimeriachalumnae_1 ENSLACT00000026689_latimeriachalumnae_1 100 +ENSDART00000028225_daniorerio_1 ENSAMXT00000002585_astyanaxmexicanus_1 100 +ENSPANT00000027631_papioanubis_1 ENSMMUT00000027387_macacamulatta_1 100 +ENSMUST00000026013_musmusculus_1 ENSRNOT00000066674_rattusnorvegicus_1 100 +ENSONIT00000016435_oreochromisniloticus_1 ENSXMAT00000001796_xiphophorusmaculatus_1 100 +ENSTNIT00000014720_tetraodonnigroviridis_1 ENSTRUT00000035430_takifugurubripes_1 100 +ENSCJAT00000058575_callithrixjacchus_1 ENSCJAT00000021080_callithrixjacchus_1 100 +ENSCJAT00000021080_callithrixjacchus_1 ENSCJAT00000058575_callithrixjacchus_1 100 +ENSMMUT00000027387_macacamulatta_1 ENSPANT00000027631_papioanubis_1 100 +ENSMGAT00000016429_meleagrisgallopavo_1 ENSGALT00000036672_gallusgallus_1 100 +ENSSSCT00000023183_susscrofa_1 ENSSSCT00000033745_susscrofa_1 100 +ENSGGOT00000000206_gorillagorilla_1 ENSPTRT00000040521_pantroglodytes_1 100 +ENSXETT00000010521_xenopustropicalis_1 ENSXETT00000010517_xenopustropicalis_1 100 +ENSCAFT00000022963_canisfamiliaris_1 ENSAMET00000018029_ailuropodamelanoleuca_1 100 +ENSGACT00000024065_gasterosteusaculeatus_1 ENSGACT00000024064_gasterosteusaculeatus_1 100 +ENSGACT00000024064_gasterosteusaculeatus_1 ENSGACT00000024065_gasterosteusaculeatus_1 100 +ENSAMET00000018029_ailuropodamelanoleuca_1 ENSCAFT00000022963_canisfamiliaris_1 100 +ENSSSCT00000033745_susscrofa_1 ENSSSCT00000023183_susscrofa_1 100 +ENSMGAT00000016431_meleagrisgallopavo_1 ENSAPLT00000013855_anasplatyrhynchos_1 100 +ENSPPYT00000023640_pongoabelii_1 ENSPPYT00000023641_pongoabelii_1 100 +ENSPPYT00000023641_pongoabelii_1 ENSPPYT00000023640_pongoabelii_1 100 +ENSTGUT00000006498_taeniopygiaguttata_1 ENSFALT00000001560_ficedulaalbicollis_1 100 +ENSLACT00000026689_latimeriachalumnae_1 ENSLACT00000014695_latimeriachalumnae_1 100 +ENSPANT00000027701_papioanubis_1 ENSPPYT00000023637_pongoabelii_1 100 +ENSPPYT00000023637_pongoabelii_1 ENSPANT00000027701_papioanubis_1 100 +ENSMUST00000040820_musmusculus_1 ENSRNOT00000044009_rattusnorvegicus_1 100 +ENSOART00000003319_ovisaries_1 ENSBTAT00000021570_bostaurus_1 100 +ENSBTAT00000021570_bostaurus_1 ENSOART00000003319_ovisaries_1 100 +ENSRNOT00000044009_rattusnorvegicus_1 ENSMUST00000040820_musmusculus_1 100 +ENSLACT00000015911_latimeriachalumnae_1 ENSLACT00000026572_latimeriachalumnae_1 100 +ENSTRUT00000011582_takifugurubripes_1 ENSTRUT00000011581_takifugurubripes_1 100 +ENSPSIT00000017443_pelodiscussinensis_1 ENSPSIT00000017454_pelodiscussinensis_1 100 +ENSTRUT00000011581_takifugurubripes_1 ENSTRUT00000011582_takifugurubripes_1 100 |