# HG changeset patch
# User fcaramia
# Date 1371446048 14400
# Node ID cd31a9b4744ec49fd3dd02535308dd0db4bc9c96
# Parent cf300f1ceeeed0ddce6961c0c5cd16df922c446a
Uploaded
diff -r cf300f1ceeee -r cd31a9b4744e contra_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/contra_wrapper.pl Mon Jun 17 01:14:08 2013 -0400
@@ -0,0 +1,94 @@
+use strict;
+use warnings;
+use File::Basename;
+use Cwd;
+use File::Path qw(make_path remove_tree);
+die qq(
+Bad numbr of inputs
+
+) if(!@ARGV);
+
+
+my $player_options = "";
+my $contra_output;
+my $contra_dir;
+
+my $dir = getcwd;
+my $variable;
+
+foreach my $input (@ARGV)
+{
+ my @tmp = split "::", $input;
+
+ if($tmp[0] eq "PLAYEROPTION")
+ {
+ $variable = $tmp[1];
+ $variable =~ s/=/ /g;
+ print "$variable\n";
+ $player_options = "$player_options $variable";
+ }
+ elsif($tmp[0] eq "CONTRAOUTPUT")
+ {
+ $contra_output = $tmp[1];
+ }
+ elsif($tmp[0] eq "CONTRADIR")
+ {
+ $contra_dir = $tmp[1];
+ }
+ else
+ {
+ die("Unknown Input: $input\n");
+ }
+}
+
+
+my $working_dir = "CONTRA_OUTPUT";
+make_path($contra_dir);
+#remove extension
+
+#run contra
+system ("contra.py -o $working_dir $player_options > /dev/null 2>&1");
+
+
+#set html
+#print "$contra_output - $working_dir\n";
+open(HTML, ">$contra_output");
+print HTML "Contra: Copy Number Analysis for Targeted ResequencingContra Output Files:
\n";
+move_files($working_dir);
+print HTML "
\n";
+close(HTML);
+
+sub move_files
+{
+ my $local_dir = $_[0];
+ opendir(DIR, $local_dir);
+ #print ("Openning: $local_dir\n");
+ my @FILES= readdir(DIR);
+ closedir(DIR);
+ foreach my $file (@FILES)
+ {
+ if ($file eq "." || $file eq "..")
+ {
+ #print ("./ or ../ skipped\n");
+ }
+ elsif (-d "$local_dir/$file")
+ {
+ #print ("moving to: $local_dir/$file\n");
+ move_files("$local_dir/$file");
+ }
+ elsif (-f "$local_dir/$file")
+ {
+ #print ("mv $local_dir/$file $contra_dir\n");
+ print HTML "$file\n";
+ system ("mv $local_dir/$file $contra_dir");
+ }
+ else
+ {
+ die("Unrecognized file generated: $file\n");
+ }
+
+
+ }
+
+}
+