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1 #!/usr/bin/env perl
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2
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3 # Execute CoNIFER plotcalls and
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4 # returns a HTML page with links to PNG plots
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5
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6 use strict;
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7 use warnings;
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8 use Getopt::Long;
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9 use File::Basename;
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10 use File::Path qw(make_path remove_tree);
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11
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12 my $command;
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13 my $dir=$ENV{'CONIFER_PATH'};
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14
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15 our ($multiple, $input, $regions, $sample, $window, $html_file, $html_folder, $verbose);
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16
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17 GetOptions('multiple'=>\$multiple, 'input=s'=>\$input, 'regions=s'=>\$regions,
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18 'sample:s'=>\$sample, 'window:i'=>\$window, 'verbose'=>\$verbose,
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19 'html_file=s'=>\$html_file, 'html_folder=s'=>\$html_folder);
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20
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21 make_path($html_folder);
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22
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23 # Build command
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24 if ($multiple){
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25 # Reformat file with regions as required by CoNIFER plotcalls
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26 system("awk '{print \$5,\$1,\$2,\$3,\$4}' OFS=\"\t\" $regions > regions_sorted");
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27
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28 $command = "python ".$dir."/conifer.py plotcalls --input $input --calls regions_sorted --window $window --outputdir $html_folder 2>&1";
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29 }else{
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30 my $sample_command = ($sample eq "") ? "" : "--sample $sample";
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31 my $plot_name = $regions;
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32 $plot_name =~ s/[:-]/_/g;
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33 $command = "python ".$dir."/conifer.py plot --input $input --region $regions $sample_command --output $html_folder/$plot_name.png 2>&1";
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34 }
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35
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36 # Run CoNIFER
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37 system($command);
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38 $verbose and print $command,"\n";
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39
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40 # Write HTML file
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41 open(HTML, ">$html_file");
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42 print HTML "<html><head><title>CoNIFER: Copy Number Analysis for Targeted Resequencing</title></head><body><h3>CoNIFER Output Files:</h3><p><ul>\n";
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43 opendir(DIR, $html_folder);
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44
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45 my @FILES= grep { /png$/ } readdir(DIR);
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46 closedir(DIR);
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47 foreach my $file (@FILES) {
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48 print HTML "<li><a href=$file>$file</a><img src=\"$file\" height=\"50\" width=\"100\"></li>\n";
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49 }
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50 print HTML "</ul></p></body></html>\n";
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51 close(HTML);
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