Mercurial > repos > jtilman > flexbar
changeset 1:a8399cb4972b
Uploaded Flexbar perl tool wrapper file flexbar.pl
| author | jtilman |
|---|---|
| date | Sun, 30 Dec 2012 14:01:39 -0500 |
| parents | 68a4edf205f3 |
| children | 609221937fae |
| files | flexbar.pl |
| diffstat | 1 files changed, 42 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.pl Sun Dec 30 14:01:39 2012 -0500 @@ -0,0 +1,42 @@ +#!/usr/bin/env perl + +# Author: Johannes T. Roehr + +use warnings; +use strict; + +my $flexbarDir = ""; + +my $pwd = $ENV{PWD}; + +my $lastIdx = $#ARGV; +my $format = $ARGV[$lastIdx]; +my $folder = $ARGV[$lastIdx - 1]; +my $id = $ARGV[$lastIdx - 2]; +my $outFile = $ARGV[$lastIdx - 3]; + +my $call = join " ", @ARGV[0..($lastIdx - 4)]; + +system $flexbarDir . $call .' --target reads > '. $outFile; + +foreach(<$pwd ."/reads"*>){ + + if(/^\.\//){ + my $file = $pwd ."/". $_; + + s/^\.\///; + my $fileType; + + $fileType = $1 if /\.(\w+)$/; + $fileType = $format if /\.\w+fast\w$/; + $fileType = 'tabular' if $fileType eq 'lengthdist'; + + s/_//g; + + my $name = "primary_". $id ."_". $_ ."_visible_". $fileType; + + rename $file, $name; + rename $name, $folder; + } +} +