Mercurial > repos > labis-app > galaxy_proteomics

annotate selectproteinids.pl @ 0:ba070efb6f78 draft

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planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
author labis-app
date Tue, 03 Jul 2018 17:34:13 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
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1 #!/usr/bin/perl -w
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3 use strict;
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4 use warnings;
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5 use FileHandle;
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8 # open file with the ids and get the lines #
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9 my $in = $ARGV[0];
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10 open INFILE, "<", $in or die $!;
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11 seek(INFILE, 0, 0);
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12
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13 my @lines = <INFILE>;
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14 shift @lines;
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16 # flag to see wheter maintain contaminants or not
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17 my $maintain_contaminants = $ARGV[1];
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18
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19 # output file with table filtered
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20 my $out = $ARGV[2];
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21 open OUTFILE, ">", $out or die $!;
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23 # select first id of first column
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24 foreach(@lines){
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25 my @vec = split ' ', $_;
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26 my @id = split ';', $vec[0];
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27 if($id[0] =~ m/^CON__/ ){
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28 if($maintain_contaminants eq "yes"){
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29 print OUTFILE $id[0] =~ s/^CON__//r, "\n";
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30 }
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31 } else{
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32 print OUTFILE $id[0], "\n";
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33 }
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34 }
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36 close INFILE;
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37 close OUTFILE;
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