Mercurial > repos > fcaramia > contra
view Contra/baseline_wrapper.pl @ 10:6a3c6e45dd4e
Deleted selected files
author | fcaramia |
---|---|
date | Sun, 02 Dec 2012 20:32:42 -0500 |
parents | 7564f3b1e675 |
children |
line wrap: on
line source
#sshpass -p pmac1512 ssh -o StrictHostkeyChecking=no galaxy@pmc-bioinf03 "gmt music play $*" #echo "gmt music play $*" use strict; use warnings; use File::Basename; use Cwd; die qq( Bad numbr of inputs ) if(!@ARGV); my $player_options = ""; my $baseline_output; my $dir = getcwd; my $variable = ""; my $files = ""; foreach my $input (@ARGV) { my @tmp = split "::", $input; if($tmp[0] eq "PLAYEROPTION") { $variable = $tmp[1]; $variable =~ s/=/ /g; $player_options = "$player_options $variable"; } elsif($tmp[0] eq "BASELINEOUTPUT") { $baseline_output = $tmp[1]; } elsif($tmp[0] eq "BAMLISTENTRY") { $files = "$files ${tmp[1]}"; } else { die("Unknown Input: $input\n"); } } my $working_dir = "BASELINE_OUTPUT"; #remove extension #Create Contra Output dir system ("mkdir $working_dir"); #run baseline system ("baseline.py --file $files --output $working_dir $player_options > /dev/null"); #Search control file in output dir opendir(DIR, $working_dir); my @FILES= readdir(DIR); foreach my $file (@FILES) { my ($filename,$directory,$extension) = fileparse($file, qr/\.[^.]*/); if ($extension eq ".txt") { system ("mv $working_dir/$file $baseline_output"); } } closedir(DIR);