# HG changeset patch # User alan-blakely # Date 1408639941 14400 # Node ID 9af08aa008de327004829d8b159317d75744f0a1 # Parent 05e720d0deb5b587af4addc7b3bf00eca610bf4c Deleted selected files 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 @@ -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; -$n=0; - -while () { - - %seq_hash{$i}=$_; - i++; - -} -close SEQ; - -while ($n < $i){ - while () { - if (/.*$seq_hash{$i}.*/) { - print OUT $1; - - } - } -n++; -} - -close (REP); -close (OUT); - - 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 @@ -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 (){ - chomp(); - $seq[$i] = $_; - $i++; -} -while (){ - $rep[$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 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 @@ -1,59 +0,0 @@ - - - - Filters a tabular file using fragment lines from a second file. - - pmatch.pl $sequences $report $output - - - - - - - - - - - - - - - - - - - - - - - -Each line from the first file is converted to a regular expression of the form .*LINE.* - -Lines from the second file that match the expression are returned. - - - - -This tool allows for partial sequences to match a larger more complete sequence. -Example: a file containing peptide sequences is used to select matching lines from a protien database in tabular form. - - -Input File: File to be filtered: - -PLPNVPQPGR >sp|P15450|ABAE_APIME Abaecin MKVVIFIFALLATICAAFAYVPLPNVPQPGRRPFPTFPGQGPFNPKIKWPQGY -PETALCARR >sp|P85829|BP01_APIME Brain peptide MVPVPVHHMADELLRNGPDTVI -EPFKISIHL >sp|P01500|APAM_APIME Apamin OS=Apis mellifera PE=1 SV=2 MISMLRCIYLFLSVILITSYFVTPVMPCNCKAPETALCARRCQQHG - >sp|P85830|DIUX_APIME Diuretic hormone class 2 OS=Apis mellifera PE=1 SV=1 GLDLGLSRGFSGSQAAKHLMGLAAANYAGGP - >sp|P84759|JELL3_APIME Jellein-3 OS=Apis mellifera PE=1 SV=1 EPFKISIHL - -Output: - ->sp|P15450|ABAE_APIME Abaecin MKVVIFIFALLATICAAFAYVPLPNVPQPGRRPFPTFPGQGPFNPKIKWPQGY ->sp|P01500|APAM_APIME Apamin OS=Apis mellifera PE=1 SV=2 MISMLRCIYLFLSVILITSYFVTPVMPCNCKAPETALCARRCQQHG ->sp|P84759|JELL3_APIME Jellein-3 OS=Apis mellifera PE=1 SV=1 EPFKISIHL - - - - - - diff -r 05e720d0deb5 -r 9af08aa008de submatch/pmatchbak.pl~ --- a/submatch/pmatchbak.pl~ Thu Aug 21 12:48:08 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -#!/usr/bin/perl -w -use JSON; - -open (SEQ, "<$ARGV[0]"); -open (REP, "<$ARGV[1]"); -open (OUT, ">$ARGV[2]"); - - - -my ($seq, $reg); - - -while () { - - $seq=$_; - - while () { - if (index($_, $seq) == -1){ - } - else{ - print OUT $_; - } - if (index($_, "NKLEGLEDALQK") != -1){ - print OUT $_; - } - print OUT $seq; - } - -} - - - - -close (SEQ); -close (REP); -close (OUT); - - 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 @@ -1,49 +0,0 @@ - - - - Filters a tabular file using fragment lines from a second file. - - pmatch.pl $sequences $report $output - - - - - - - - - - - - - - - - - - - - - - - -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. - - - - - - - -