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comparison Contra/baseline_wrapper.pl @ 0:7564f3b1e675

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author fcaramia
date Thu, 13 Sep 2012 02:31:43 -0400
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-1:000000000000 0:7564f3b1e675
1 #sshpass -p pmac1512 ssh -o StrictHostkeyChecking=no galaxy@pmc-bioinf03 "gmt music play $*"
2 #echo "gmt music play $*"
3
4
5 use strict;
6 use warnings;
7 use File::Basename;
8 use Cwd;
9 die qq(
10 Bad numbr of inputs
11
12 ) if(!@ARGV);
13
14
15 my $player_options = "";
16 my $baseline_output;
17
18 my $dir = getcwd;
19 my $variable = "";
20 my $files = "";
21 foreach my $input (@ARGV)
22 {
23 my @tmp = split "::", $input;
24
25 if($tmp[0] eq "PLAYEROPTION")
26 {
27 $variable = $tmp[1];
28 $variable =~ s/=/ /g;
29 $player_options = "$player_options $variable";
30 }
31 elsif($tmp[0] eq "BASELINEOUTPUT")
32 {
33 $baseline_output = $tmp[1];
34 }
35 elsif($tmp[0] eq "BAMLISTENTRY")
36 {
37 $files = "$files ${tmp[1]}";
38 }
39 else
40 {
41 die("Unknown Input: $input\n");
42 }
43 }
44
45
46 my $working_dir = "BASELINE_OUTPUT";
47 #remove extension
48
49 #Create Contra Output dir
50 system ("mkdir $working_dir");
51
52 #run baseline
53
54 system ("baseline.py --file $files --output $working_dir $player_options > /dev/null");
55
56 #Search control file in output dir
57 opendir(DIR, $working_dir);
58 my @FILES= readdir(DIR);
59 foreach my $file (@FILES)
60 {
61 my ($filename,$directory,$extension) = fileparse($file, qr/\.[^.]*/);
62 if ($extension eq ".txt")
63 {
64 system ("mv $working_dir/$file $baseline_output");
65 }
66 }
67 closedir(DIR);
68