# HG changeset patch
# User alan-blakely
# Date 1408639688 14400
# Node ID 05e720d0deb5b587af4addc7b3bf00eca610bf4c

Uploaded

diff -r 000000000000 -r 05e720d0deb5 submatch/partial.pl~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch/partial.pl~	Thu Aug 21 12:48:08 2014 -0400
@@ -0,0 +1,35 @@
+#!/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);
+
+    
diff -r 000000000000 -r 05e720d0deb5 submatch/pmatch.pl~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch/pmatch.pl~	Thu Aug 21 12:48:08 2014 -0400
@@ -0,0 +1,40 @@
+#!/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]"); 
+    
diff -r 000000000000 -r 05e720d0deb5 submatch/pmatch.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch/pmatch.xml~	Thu Aug 21 12:48:08 2014 -0400
@@ -0,0 +1,59 @@
+
+<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>
diff -r 000000000000 -r 05e720d0deb5 submatch/pmatchbak.pl~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch/pmatchbak.pl~	Thu Aug 21 12:48:08 2014 -0400
@@ -0,0 +1,38 @@
+#!/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);
+
+    
diff -r 000000000000 -r 05e720d0deb5 submatch/submatch.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch/submatch.pl	Thu Aug 21 12:48:08 2014 -0400
@@ -0,0 +1,41 @@
+#!/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++;
+	}
+	$l++;
+}
+
+
+
+close (SEQ);
+close (REP);
+close (OUT);
+
+#optional: remove duplicate lines using server-side shell command
+system("sort", "-u", "-o", "$ARGV[2]", "$ARGV[2]"); 
+    
diff -r 000000000000 -r 05e720d0deb5 submatch/submatch.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch/submatch.xml	Thu Aug 21 12:48:08 2014 -0400
@@ -0,0 +1,49 @@
+
+<tool id="pmatch" name="Filter by Substring Match">
+
+    <description>This tool allows for partial sequences to match lines containing a larger, more complete sequence. </description>
+
+    <command interpreter="perl">submatch.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="submatch_input.tab"/>
+      <param name="report" value="submatch_input2.tab"/>
+      <output name="output" file="submatch_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>
diff -r 000000000000 -r 05e720d0deb5 submatch/submatch.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/submatch/submatch.xml~	Thu Aug 21 12:48:08 2014 -0400
@@ -0,0 +1,49 @@
+
+<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>