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comparison flexbar.pl @ 1:a8399cb4972b

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Uploaded Flexbar perl tool wrapper file flexbar.pl
author jtilman
date Sun, 30 Dec 2012 14:01:39 -0500
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children f0bdf862ba39
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0:68a4edf205f3 1:a8399cb4972b
1 #!/usr/bin/env perl
2
3 # Author: Johannes T. Roehr
4
5 use warnings;
6 use strict;
7
8 my $flexbarDir = "";
9
10 my $pwd = $ENV{PWD};
11
12 my $lastIdx = $#ARGV;
13 my $format = $ARGV[$lastIdx];
14 my $folder = $ARGV[$lastIdx - 1];
15 my $id = $ARGV[$lastIdx - 2];
16 my $outFile = $ARGV[$lastIdx - 3];
17
18 my $call = join " ", @ARGV[0..($lastIdx - 4)];
19
20 system $flexbarDir . $call .' --target reads > '. $outFile;
21
22 foreach(<$pwd ."/reads"*>){
23
24 if(/^\.\//){
25 my $file = $pwd ."/". $_;
26
27 s/^\.\///;
28 my $fileType;
29
30 $fileType = $1 if /\.(\w+)$/;
31 $fileType = $format if /\.\w+fast\w$/;
32 $fileType = 'tabular' if $fileType eq 'lengthdist';
33
34 s/_//g;
35
36 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
37
38 rename $file, $name;
39 rename $name, $folder;
40 }
41 }
42