Mercurial > repos > bzonnedda > conifer2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/conifer_wrapper.pl	Mon Feb 06 10:56:08 2017 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/env perl
+
+# Execute CoNIFER plotcalls and
+# returns a HTML page with links to PNG plots
+
+use strict;
+use warnings;
+use Getopt::Long;
+use File::Basename;
+use File::Path qw(make_path remove_tree);
+
+my $command;
+my $dir=$ENV{'CONIFER_PATH'};
+
+our ($multiple, $input, $regions, $sample, $window, $html_file, $html_folder, $verbose);
+
+GetOptions('multiple'=>\$multiple, 'input=s'=>\$input, 'regions=s'=>\$regions,
+    'sample:s'=>\$sample, 'window:i'=>\$window, 'verbose'=>\$verbose,
+    'html_file=s'=>\$html_file, 'html_folder=s'=>\$html_folder);
+
+make_path($html_folder);
+
+# Build command
+if ($multiple){
+    # Reformat file with regions as required by CoNIFER plotcalls
+    system("awk '{print \$5,\$1,\$2,\$3,\$4}' OFS=\"\t\" $regions > regions_sorted");
+
+    $command = "python ".$dir."/conifer.py plotcalls --input $input --calls regions_sorted --window $window --outputdir $html_folder 2>&1";
+}else{
+    my $sample_command = ($sample eq "") ? "" : "--sample $sample";
+    my $plot_name = $regions;
+    $plot_name =~ s/[:-]/_/g;
+    $command = "python ".$dir."/conifer.py plot --input $input --region $regions $sample_command --output $html_folder/$plot_name.png 2>&1";
+}
+
+# Run CoNIFER
+system($command);
+$verbose and print $command,"\n";
+
+# Write HTML file
+open(HTML, ">$html_file");
+print HTML "<html><head><title>CoNIFER: Copy Number Analysis for Targeted Resequencing</title></head><body><h3>CoNIFER Output Files:</h3><p><ul>\n";
+opendir(DIR, $html_folder);
+
+my @FILES= grep { /png$/ }  readdir(DIR);
+closedir(DIR);
+foreach my $file (@FILES) {
+    print HTML "<li><a href=$file>$file</a><img src=\"$file\" height=\"50\" width=\"100\"></li>\n";
+}
+print HTML "</ul></p></body></html>\n";
+close(HTML);