Mercurial > repos > alan-blakely > filter_by_substring_match

--- a/submatch/partial.pl~	Thu Aug 21 12:48:08 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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);
-
-
--- a/submatch/pmatch.pl~	Thu Aug 21 12:48:08 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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]");
-
--- a/submatch/pmatch.xml~	Thu Aug 21 12:48:08 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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 $output </command>
-
-    <inputs>
-
-	<param format="tabular" name="sequences" type="data" label="Tabular file containing list to filter on."/>
-	<param format="tabular" name="report" type="data" label="Tabular file to be filtered."/>
-
-    </inputs>
-
-    <outputs>
-        <data format="tabular" name="output" />
-    </outputs>
-  <tests>
-    <test>
-      <param name="sequences" value="pmatch_input.tab"/>
-      <param name="report" value="pmatch_input2.tab"/>
-      <output name="output" file="pmatch_output.tab"/>
-    </test>
-  </tests>
-
-<help>
-
-
-
-Each line from the first file is converted to a regular expression of the form .*LINE.*
-
-Lines from the second file that match the expression are returned.
-
-
-
-
-This tool allows for partial sequences to match a larger more complete sequence.
-Example: a file containing peptide sequences is used to select matching lines from a protien database in tabular form.
-
-
-Input File:	File to be filtered:
-
-PLPNVPQPGR	>sp|P15450|ABAE_APIME Abaecin MKVVIFIFALLATICAAFAYV<b>PLPNVPQPGR</b>RPFPTFPGQGPFNPKIKWPQGY
-PETALCARR	>sp|P85829|BP01_APIME Brain peptide MVPVPVHHMADELLRNGPDTVI
-EPFKISIHL	>sp|P01500|APAM_APIME Apamin OS=Apis mellifera PE=1 SV=2 MISMLRCIYLFLSVILITSYFVTPVMPCNCKA<b>PETALCARR</b>CQQHG
-		>sp|P85830|DIUX_APIME Diuretic hormone class 2 OS=Apis mellifera PE=1 SV=1 GLDLGLSRGFSGSQAAKHLMGLAAANYAGGP
-		>sp|P84759|JELL3_APIME Jellein-3 OS=Apis mellifera PE=1 SV=1 <b>EPFKISIHL</b>
-
-Output:
-
->sp|P15450|ABAE_APIME Abaecin MKVVIFIFALLATICAAFAYVPLPNVPQPGRRPFPTFPGQGPFNPKIKWPQGY
->sp|P01500|APAM_APIME Apamin OS=Apis mellifera PE=1 SV=2 MISMLRCIYLFLSVILITSYFVTPVMPCNCKAPETALCARRCQQHG
->sp|P84759|JELL3_APIME Jellein-3 OS=Apis mellifera PE=1 SV=1 EPFKISIHL
-
-
-
-</help>
-
-</tool>
--- a/submatch/pmatchbak.pl~	Thu Aug 21 12:48:08 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/perl -w
-use JSON;
-
-open (SEQ, "<$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);
-
-
--- a/submatch/submatch.xml~	Thu Aug 21 12:48:08 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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>