| Next changeset 1:fd11653657f9 (2016-12-12) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty |
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added:
blast_parser.pl blast_parser.xml test-data/input.tabular test-data/output.tabular |
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| diff -r 000000000000 -r 87eda806422d blast_parser.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast_parser.pl Mon Dec 12 07:13:57 2016 -0500 |
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| @@ -0,0 +1,43 @@ +#!/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 000000000000 -r 87eda806422d blast_parser.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast_parser.xml Mon Dec 12 07:13:57 2016 -0500 |
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| @@ -0,0 +1,35 @@ +<tool id="blast_parser" name="blast_parser" version="0.1.1"> + <description> + Convert 12- or 24-column BLAST output into 3-column hcluster_sg input + </description> + + <command> +<![CDATA[ +perl $__tool_directory__/blast_parser.pl +$input +> $output +]]> + </command> + + <inputs> + <param name="input" type="data" format="tabular" label="Tabular data" help="BLAST 12 column tabular format data"/> + </inputs> + + <outputs> + <data name="output" format="tabular" label="$tool.name on ${on_string}" /> + </outputs> + + <tests> + <test> + <param name="input" ftype="tabular" value="input.tabular" /> + <output name="output" file="output.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. +]]> + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 87eda806422d test-data/input.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.tabular Mon Dec 12 07:13:57 2016 -0500 |
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| b'@@ -0,0 +1,321 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| diff -r 000000000000 -r 87eda806422d test-data/output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tabular Mon Dec 12 07:13:57 2016 -0500 |
| b |
| b'@@ -0,0 +1,161 @@\n+ENSFCAT00000013089_feliscatus_1\tENSCAFT00000022939_canisfamiliaris_1\t100\n+ENSCAFT00000022939_canisfamiliaris_1\tENSFCAT00000013089_feliscatus_1\t100\n+ENSAMXT00000002585_astyanaxmexicanus_1\tENSDART00000028225_daniorerio_1\t100\n+ENSPCAT00000008534_procaviacapensis_1\tENST00000378069_homosapiens_1\t100\n+ENSLOCT00000017020_lepisosteusoculatus_1\tENSLACT00000026689_latimeriachalumnae_1\t100\n+ENSCPOT00000000986_caviaporcellus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSTGUT00000016508_taeniopygiaguttata_1\tENSTGUT00000006603_taeniopygiaguttata_1\t100\n+ENSPFOT00000010657_poeciliaformosa_1\tENSXMAT00000001796_xiphophorusmaculatus_1\t100\n+ENSDNOT00000016434_dasypusnovemcinctus_1\tENSDNOT00000036768_dasypusnovemcinctus_1\t100\n+ENSPMAT00000010398_petromyzonmarinus_1\tENSLACT00000015911_latimeriachalumnae_1\t64\n+ENSAMET00000018099_ailuropodamelanoleuca_1\tENSCAFT00000022939_canisfamiliaris_1\t100\n+ENSEEUT00000005606_erinaceuseuropaeus_1\tENSMPUT00000012759_mustelaputoriusfuro_1\t100\n+ENSSHAT00000006757_sarcophilusharrisii_1\tENSMODT00000026841_monodelphisdomestica_1\t100\n+ENSPSIT00000017454_pelodiscussinensis_1\tENSPSIT00000017443_pelodiscussinensis_1\t100\n+ENSPFOT00000022544_poeciliaformosa_1\tENSXMAT00000001796_xiphophorusmaculatus_1\t100\n+ENSMICT00000002052_microcebusmurinus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSMICT00000002052_microcebusmurinus_1\tENSCAFT00000022963_canisfamiliaris_1\t46\n+ENSRNOT00000066674_rattusnorvegicus_1\tENSMUST00000026013_musmusculus_1\t100\n+ENSFCAT00000013090_feliscatus_1\tENSAMET00000018029_ailuropodamelanoleuca_1\t100\n+ENSONIT00000020514_oreochromisniloticus_1\tENSPFOT00000009022_poeciliaformosa_1\t100\n+ENSLACT00000026572_latimeriachalumnae_1\tENSLACT00000015911_latimeriachalumnae_1\t100\n+ENSPMAT00000003449_petromyzonmarinus_1\tENSGGOT00000000206_gorillagorilla_1\t100\n+ENSSART00000014230_sorexaraneus_1\tENSSTOT00000004965_ictidomystridecemlineatus_1\t100\n+ENSSART00000014230_sorexaraneus_1\tENSSTOT00000004965_ictidomystridecemlineatus_1\t44\n+ENSBTAT00000001698_bostaurus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSTBET00000006983_tupaiabelangeri_1\tENSAMET00000018099_ailuropodamelanoleuca_1\t100\n+ENSLACT00000014274_latimeriachalumnae_1\tENSLACT00000026689_latimeriachalumnae_1\t100\n+ENSPFOT00000009022_poeciliaformosa_1\tENSTRUT00000035430_takifugurubripes_1\t100\n+ENSSHAT00000005478_sarcophilusharrisii_1\tENSMODT00000026840_monodelphisdomestica_1\t100\n+ENSTBET00000000639_tupaiabelangeri_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSTGUT00000006603_taeniopygiaguttata_1\tENSFALT00000001591_ficedulaalbicollis_1\t100\n+ENSSART00000014241_sorexaraneus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSPVAT00000011223_pteropusvampyrus_1\tENSCAFT00000022939_canisfamiliaris_1\t100\n+ENSPVAT00000011226_pteropusvampyrus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSAPLT00000013117_anasplatyrhynchos_1\tENSMGAT00000016429_meleagrisgallopavo_1\t100\n+ENSFALT00000001560_ficedulaalbicollis_1\tENSTGUT00000006498_taeniopygiaguttata_1\t100\n+ENST00000338702_homosapiens_1\tENSPPYT00000023637_pongoabelii_1\t100\n+ENSXMAT00000001796_xiphophorusmaculatus_1\tENSONIT00000016435_oreochromisniloticus_1\t100\n+ENSSSCT00000013404_susscrofa_1\tENSPPYT00000023637_pongoabelii_1\t100\n+ENSGALT00000036672_gallusgallus_1\tENSMGAT00000016429_meleagrisgallopavo_1\t100\n+ENSOPRT00000017156_ochotonaprinceps_1\tENSOCUT00000001438_oryctolaguscuniculus_1\t100\n+ENSOPRT00000017156_ochotonaprinceps_1\tENSOCUT00000001438_oryctolaguscuniculus_1\t17\n+ENSSTOT00000004988_ictidomystridecemlineatus_1\tENSPANT00000027606_papioanubis_1\t100\n+ENSECAT00000024641_equuscaballus_1\tENSCAFT00000022939_canisfamiliaris_1\t100\n+ENSAPLT00000013855_anasplatyrhynchos_1\tENSMGAT00000016431_meleagrisgallopavo_1\t100\n+ENSDART00000132084_daniorerio_1\tENSDART00000160057_daniorerio_1\t100\n+ENSNLET00000003021_nomascusleucogenys_1\tENSPPYT00000023637_pongoabelii_1\t100\n+ENSPTRT00000040521_pantroglodytes_1\tENSGGOT00000000206_gorillagorilla_1\t100\n+ENSPTRT00000040520_pantroglodytes_1\tENSPPYT00000023637_pongoabelii_1\t100\n+ENSMEUT0000000374'..b'100\n+ENSSSCT00000023183_susscrofa_1\tENSSSCT00000033745_susscrofa_1\t100\n+ENSETET00000008126_echinopstelfairi_1\tENSLAFT00000000504_loxodontaafricana_1\t100\n+ENSGMOT00000015214_gadusmorhua_1\tENSGACT00000012444_gasterosteusaculeatus_1\t100\n+ENSGGOT00000000206_gorillagorilla_1\tENSPTRT00000040521_pantroglodytes_1\t100\n+ENSNLET00000003121_nomascusleucogenys_1\tENSGGOT00000000206_gorillagorilla_1\t100\n+ENSXETT00000010521_xenopustropicalis_1\tENSXETT00000010517_xenopustropicalis_1\t100\n+ENSCJAT00000020968_callithrixjacchus_1\tENSCJAT00000055001_callithrixjacchus_1\t100\n+ENSTTRT00000009129_tursiopstruncatus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSCAFT00000022963_canisfamiliaris_1\tENSAMET00000018029_ailuropodamelanoleuca_1\t100\n+ENSGGOT00000008973_gorillagorilla_1\tENSPPYT00000023637_pongoabelii_1\t100\n+ENSOGAT00000031973_otolemurgarnettii_1\tENSOGAT00000005620_otolemurgarnettii_1\t100\n+ENSGACT00000024065_gasterosteusaculeatus_1\tENSGACT00000024064_gasterosteusaculeatus_1\t100\n+ENSGACT00000024064_gasterosteusaculeatus_1\tENSGACT00000024065_gasterosteusaculeatus_1\t100\n+ENSAMET00000018029_ailuropodamelanoleuca_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSECAT00000001417_equuscaballus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSTSYT00000009875_tarsiussyrichta_1\tENSGGOT00000000206_gorillagorilla_1\t100\n+ENSSSCT00000033745_susscrofa_1\tENSSSCT00000023183_susscrofa_1\t100\n+ENSOART00000003571_ovisaries_1\tENSBTAT00000001698_bostaurus_1\t100\n+ENSMGAT00000016431_meleagrisgallopavo_1\tENSAPLT00000013855_anasplatyrhynchos_1\t100\n+ENSCHOT00000008295_choloepushoffmanni_1\tENSECAT00000024641_equuscaballus_1\t100\n+ENSOCUT00000001433_oryctolaguscuniculus_1\tENSPPYT00000023637_pongoabelii_1\t100\n+ENSPPYT00000023640_pongoabelii_1\tENSPPYT00000023641_pongoabelii_1\t100\n+ENSPPYT00000023641_pongoabelii_1\tENSPPYT00000023640_pongoabelii_1\t100\n+ENSOGAT00000030491_otolemurgarnettii_1\tENSCAFT00000022939_canisfamiliaris_1\t100\n+ENSCHOT00000004109_choloepushoffmanni_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSOCUT00000001438_oryctolaguscuniculus_1\tENSCAFT00000022963_canisfamiliaris_1\t100\n+ENSTGUT00000006498_taeniopygiaguttata_1\tENSFALT00000001560_ficedulaalbicollis_1\t100\n+ENSLACT00000026689_latimeriachalumnae_1\tENSLACT00000014695_latimeriachalumnae_1\t100\n+ENSPANT00000027701_papioanubis_1\tENSPPYT00000023637_pongoabelii_1\t100\n+ENSPPYT00000023637_pongoabelii_1\tENSPANT00000027701_papioanubis_1\t100\n+ENSMUST00000040820_musmusculus_1\tENSRNOT00000044009_rattusnorvegicus_1\t100\n+ENSLAFT00000027936_loxodontaafricana_1\tENSLAFT00000015029_loxodontaafricana_1\t100\n+ENSPSIT00000016442_pelodiscussinensis_1\tENSAPLT00000013117_anasplatyrhynchos_1\t100\n+ENSOART00000003319_ovisaries_1\tENSBTAT00000021570_bostaurus_1\t100\n+ENSMMUT00000046681_macacamulatta_1\tENSPANT00000027701_papioanubis_1\t28\n+ENSMMUT00000046680_macacamulatta_1\tENSCSAT00000012035_chlorocebussabaeus_1\t44\n+ENSBTAT00000021570_bostaurus_1\tENSOART00000003319_ovisaries_1\t100\n+ENST00000378069_homosapiens_1\tENSGGOT00000000206_gorillagorilla_1\t100\n+ENSPANT00000027606_papioanubis_1\tENSPANT00000027631_papioanubis_1\t100\n+ENSLAFT00000000504_loxodontaafricana_1\tENSECAT00000024641_equuscaballus_1\t100\n+ENSPCAT00000006605_procaviacapensis_1\tENSLAFT00000000504_loxodontaafricana_1\t100\n+ENSLOCT00000002323_lepisosteusoculatus_1\tENSDART00000028225_daniorerio_1\t100\n+ENSMUST00000173143_musmusculus_1\tENSMUST00000163344_musmusculus_1\t5\n+ENSRNOT00000044009_rattusnorvegicus_1\tENSMUST00000040820_musmusculus_1\t100\n+ENSMODT00000026841_monodelphisdomestica_1\tENSCAFT00000022939_canisfamiliaris_1\t100\n+ENSLACT00000015911_latimeriachalumnae_1\tENSLACT00000026572_latimeriachalumnae_1\t100\n+ENSSSCT00000035258_susscrofa_1\tENSSSCT00000013404_susscrofa_1\t97\n+ENSTRUT00000011582_takifugurubripes_1\tENSTRUT00000011581_takifugurubripes_1\t100\n+ENSPSIT00000017443_pelodiscussinensis_1\tENSPSIT00000017454_pelodiscussinensis_1\t100\n+ENSTRUT00000011580_takifugurubripes_1\tENSTRUT00000011581_takifugurubripes_1\t100\n+ENSTRUT00000011581_takifugurubripes_1\tENSTRUT00000011582_takifugurubripes_1\t100\n' |