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comparison flexbar.pl @ 11:52c5e53aff28

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Revised perl wrapper.
author jtilman
date Wed, 02 Jan 2013 12:54:28 +0100
parents f0bdf862ba39
children 4cbf6c6d2f2b
comparison
equal deleted inserted replaced
10:f0bdf862ba39 11:52c5e53aff28
3 # Author: Johannes T. Roehr 3 # Author: Johannes T. Roehr
4 4
5 use warnings; 5 use warnings;
6 use strict; 6 use strict;
7 7
8 my $format = pop @ARGV;
9 my $folder = pop @ARGV;
10 my $id = pop @ARGV;
11 my $outFile = pop @ARGV;
12 8
13 my $call = join " ", @ARGV; 9 my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV];
10
11 my $call = join " ", @ARGV[0..($#ARGV - 4)];
14 12
15 system $call .' --target reads > '. $outFile and exit 1; 13 system $call .' --target reads > '. $outFile and exit 1;
16 14
17 15
18 foreach(<reads*>){ 16 foreach(<reads*>){
21 19
22 $fileType = $1 if /\.(\w+)$/; 20 $fileType = $1 if /\.(\w+)$/;
23 $fileType = $format if /\.\w+fast\w$/; 21 $fileType = $format if /\.\w+fast\w$/;
24 $fileType = 'tabular' if $fileType eq 'lengthdist'; 22 $fileType = 'tabular' if $fileType eq 'lengthdist';
25 23
24 my $file = $_;
25
26 s/_//g; 26 s/_//g;
27 27
28 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType; 28 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
29 29
30 rename $_, $name; 30 rename $file, $name;
31 rename $name, $folder; 31 rename $name, $folder;
32 } 32 }
33 33