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comparison flexbar.pl @ 10:f0bdf862ba39

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Simplified perl wrapper.
author jtilman
date Mon, 31 Dec 2012 18:40:01 +0100
parents a8399cb4972b
children 52c5e53aff28
comparison
equal deleted inserted replaced
9:cb6deaad121f 10:f0bdf862ba39
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 $flexbarDir = ""; 8 my $format = pop @ARGV;
9 my $folder = pop @ARGV;
10 my $id = pop @ARGV;
11 my $outFile = pop @ARGV;
9 12
10 my $pwd = $ENV{PWD}; 13 my $call = join " ", @ARGV;
11 14
12 my $lastIdx = $#ARGV; 15 system $call .' --target reads > '. $outFile and exit 1;
13 my $format = $ARGV[$lastIdx];
14 my $folder = $ARGV[$lastIdx - 1];
15 my $id = $ARGV[$lastIdx - 2];
16 my $outFile = $ARGV[$lastIdx - 3];
17 16
18 my $call = join " ", @ARGV[0..($lastIdx - 4)];
19 17
20 system $flexbarDir . $call .' --target reads > '. $outFile; 18 foreach(<reads*>){
21
22 foreach(<$pwd ."/reads"*>){
23 19
24 if(/^\.\//){ 20 my $fileType;
25 my $file = $pwd ."/". $_; 21
26 22 $fileType = $1 if /\.(\w+)$/;
27 s/^\.\///; 23 $fileType = $format if /\.\w+fast\w$/;
28 my $fileType; 24 $fileType = 'tabular' if $fileType eq 'lengthdist';
29 25
30 $fileType = $1 if /\.(\w+)$/; 26 s/_//g;
31 $fileType = $format if /\.\w+fast\w$/; 27
32 $fileType = 'tabular' if $fileType eq 'lengthdist'; 28 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
33 29
34 s/_//g; 30 rename $_, $name;
35 31 rename $name, $folder;
36 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
37
38 rename $file, $name;
39 rename $name, $folder;
40 }
41 } 32 }
42 33