| Previous changeset 7:589b4866f537 (2012-12-30) Next changeset 9:cb6deaad121f (2012-12-31) |
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Commit message:
Uploaded Flexbar perl tool wrapper file flexbar.pl |
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added:
flexbar.pl |
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| diff -r 589b4866f537 -r f3b45062843e flexbar.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar.pl Sun Dec 30 18:45:11 2012 -0500 |
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| @@ -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; + } +} + |