| Previous changeset 0:05e720d0deb5 (2014-08-21) Next changeset 2:397067d90a77 (2014-08-21) |
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Commit message:
Deleted selected files |
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removed:
submatch/partial.pl~ submatch/pmatch.pl~ submatch/pmatch.xml~ submatch/pmatchbak.pl~ submatch/submatch.xml~ |
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| diff -r 05e720d0deb5 -r 9af08aa008de submatch/partial.pl~ --- a/submatch/partial.pl~ Thu Aug 21 12:48:08 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,35 +0,0 @@ -#!/usr/bin/perl -w -use JSON; - -open (SEQ, "<$ARGV[0]"); -open (REP, "<$ARGV[1]"); -open (OUT, ">$ARGV[2]"); - - - -my (%seq_hash, $i, $n); -$i=0; -$n=0; - -while (<SEQ>) { - - %seq_hash{$i}=$_; - i++; - -} -close SEQ; - -while ($n < $i){ - while (<REP>) { - if (/.*$seq_hash{$i}.*/) { - print OUT $1; - - } - } -n++; -} - -close (REP); -close (OUT); - - |
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| diff -r 05e720d0deb5 -r 9af08aa008de submatch/pmatch.pl~ --- a/submatch/pmatch.pl~ Thu Aug 21 12:48:08 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,40 +0,0 @@ -#!/usr/bin/perl -w -use strict; -my (@seq, @rep, $i, $n, $l, $t); - -open (SEQ, "<$ARGV[0]"); -open (REP, "<$ARGV[1]"); -open (OUT, ">$ARGV[2]"); - - -$i=$n=$l=0; - - - -while (<SEQ>){ - chomp(); - $seq[$i] = $_; - $i++; -} -while (<REP>){ - $rep[$n] = $_; - $n++; - -} -while ($l < $i){ - $t=0; - while ($t < $n){ - print OUT $rep[$t] if $rep[$t] =~ /$seq[$l]/; - $t++; - } - $l++; -} - - - -close (SEQ); -close (REP); -close (OUT); - -system("sort", "-u", "-o", "$ARGV[2]", "$ARGV[2]"); - |
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| diff -r 05e720d0deb5 -r 9af08aa008de submatch/pmatch.xml~ --- a/submatch/pmatch.xml~ Thu Aug 21 12:48:08 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,59 +0,0 @@ - -<tool id="pmatch" name="Filter by Partial Match"> - - <description>Filters a tabular file using fragment lines from a second file. </description> - - <command interpreter="perl">pmatch.pl $sequences $report $output </command> - - <inputs> - - <param format="tabular" name="sequences" type="data" label="Tabular file containing list to filter on."/> - <param format="tabular" name="report" type="data" label="Tabular file to be filtered."/> - - </inputs> - - <outputs> - <data format="tabular" name="output" /> - </outputs> - <tests> - <test> - <param name="sequences" value="pmatch_input.tab"/> - <param name="report" value="pmatch_input2.tab"/> - <output name="output" file="pmatch_output.tab"/> - </test> - </tests> - -<help> - - - -Each line from the first file is converted to a regular expression of the form .*LINE.* - -Lines from the second file that match the expression are returned. - - - - -This tool allows for partial sequences to match a larger more complete sequence. -Example: a file containing peptide sequences is used to select matching lines from a protien database in tabular form. - - -Input File: File to be filtered: - -PLPNVPQPGR >sp|P15450|ABAE_APIME Abaecin MKVVIFIFALLATICAAFAYV<b>PLPNVPQPGR</b>RPFPTFPGQGPFNPKIKWPQGY -PETALCARR >sp|P85829|BP01_APIME Brain peptide MVPVPVHHMADELLRNGPDTVI -EPFKISIHL >sp|P01500|APAM_APIME Apamin OS=Apis mellifera PE=1 SV=2 MISMLRCIYLFLSVILITSYFVTPVMPCNCKA<b>PETALCARR</b>CQQHG - >sp|P85830|DIUX_APIME Diuretic hormone class 2 OS=Apis mellifera PE=1 SV=1 GLDLGLSRGFSGSQAAKHLMGLAAANYAGGP - >sp|P84759|JELL3_APIME Jellein-3 OS=Apis mellifera PE=1 SV=1 <b>EPFKISIHL</b> - -Output: - ->sp|P15450|ABAE_APIME Abaecin MKVVIFIFALLATICAAFAYVPLPNVPQPGRRPFPTFPGQGPFNPKIKWPQGY ->sp|P01500|APAM_APIME Apamin OS=Apis mellifera PE=1 SV=2 MISMLRCIYLFLSVILITSYFVTPVMPCNCKAPETALCARRCQQHG ->sp|P84759|JELL3_APIME Jellein-3 OS=Apis mellifera PE=1 SV=1 EPFKISIHL - - - -</help> - -</tool> |
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| diff -r 05e720d0deb5 -r 9af08aa008de submatch/pmatchbak.pl~ --- a/submatch/pmatchbak.pl~ Thu Aug 21 12:48:08 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,38 +0,0 @@ -#!/usr/bin/perl -w -use JSON; - -open (SEQ, "<$ARGV[0]"); -open (REP, "<$ARGV[1]"); -open (OUT, ">$ARGV[2]"); - - - -my ($seq, $reg); - - -while (<SEQ>) { - - $seq=$_; - - while (<REP>) { - if (index($_, $seq) == -1){ - } - else{ - print OUT $_; - } - if (index($_, "NKLEGLEDALQK") != -1){ - print OUT $_; - } - print OUT $seq; - } - -} - - - - -close (SEQ); -close (REP); -close (OUT); - - |
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| diff -r 05e720d0deb5 -r 9af08aa008de submatch/submatch.xml~ --- a/submatch/submatch.xml~ Thu Aug 21 12:48:08 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,49 +0,0 @@ - -<tool id="pmatch" name="Filter by Partial Match"> - - <description>Filters a tabular file using fragment lines from a second file. </description> - - <command interpreter="perl">pmatch.pl $sequences $report $output </command> - - <inputs> - - <param format="tabular" name="sequences" type="data" label="Tabular file containing list to filter on."/> - <param format="tabular" name="report" type="data" label="Tabular file to be filtered."/> - - </inputs> - - <outputs> - <data format="tabular" name="output" /> - </outputs> - <tests> - <test> - <param name="sequences" value="pmatch_input.tab"/> - <param name="report" value="pmatch_input2.tab"/> - <output name="output" file="pmatch_output.tab"/> - </test> - </tests> - -<help> - - - -Each line from the list file is converted to a regular expression of the form .*LINE.* - - - -Lines from the second file that match the expression are returned. - - - - -This tool allows for partial sequences to match lines containing a larger more complete sequence. - -Example: a file containing fragment amino acid sequences is used to select corresponding lines from a peptide report. - - - - - -</help> - -</tool> |