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annotate contra_wrapper.pl @ 27:0bf826f62f04 default tip

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fixed toolshed not filling fields
author Franco Caramia <franco.caramia@petermac.org>
date Wed, 04 Jun 2014 11:04:17 +1000
parents 00278c5fe014
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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Franco Caramia <franco.caramia@petermac.org>
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1 use strict;
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2 use warnings;
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4 use File::Find;
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5 use File::Path qw(make_path);
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6 use File::Spec;
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9 die "Bad number of inputs" if(!@ARGV);
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11 my $player_options = "";
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12 my $contra_output;
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13 my $contra_dir;
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17 foreach my $input (@ARGV)
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18 {
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19 my @tmp = split "::", $input;
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21 if($tmp[0] eq "PLAYEROPTION")
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22 {
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23 my $variable = $tmp[1];
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24 $variable =~ s/=/ /g;
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26 $player_options = "$player_options $variable";
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27 }
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28 elsif($tmp[0] eq "CONTRAOUTPUT")
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29 {
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30 $contra_output = $tmp[1];
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31 }
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32 elsif($tmp[0] eq "CONTRADIR")
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33 {
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34 $contra_dir = $tmp[1];
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35 }
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36 else
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37 {
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38 die("Unknown input: $input\n");
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39 }
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40 }
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44 my $working_dir = File::Spec->catfile($contra_dir, 'CONTRA_OUTPUT');
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45 make_path($contra_dir);
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46 #remove extension
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48 my $cmd = "contra.py -o $working_dir $player_options";
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49 print "Command to be executed: $cmd\n";
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50 system($cmd);
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52 #set html
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53 #print "$contra_output - $working_dir\n";
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54 open(HTML, ">$contra_output");
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55 print HTML "<html><head><title>Contra: Copy Number Analysis for Targeted Resequencing</title></head><body><h3>Contra Output Files:</h3><p><ul>\n";
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56 find({wanted => \&add_file, preprocess => sub {sort @_}}, $working_dir);
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57 print HTML "</ul></p>\n";
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58 close(HTML);
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60 sub add_file {
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61 if (-f $File::Find::name) {
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62 my $rel_path = File::Spec->abs2rel($File::Find::name, $working_dir);
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63 print ("adding $rel_path\n");
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64 print HTML "<li><a href=\"CONTRA_OUTPUT/$rel_path\">$rel_path</a></li>\n";
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65 }
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66 }
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