Mercurial > repos > jtilman > flexbar
annotate flexbar.pl @ 12:4cbf6c6d2f2b
Fixed issue where adapter removal can not be performed and further minor issues.
| author | jtilman |
|---|---|
| date | Thu, 17 Jan 2013 18:09:44 +0100 |
| parents | 52c5e53aff28 |
| children | 346a2b0979ea |
| rev | line source |
|---|---|
| 1 | 1 #!/usr/bin/env perl |
| 2 | |
| 3 # Author: Johannes T. Roehr | |
| 4 | |
| 5 use warnings; | |
| 6 use strict; | |
| 7 | |
| 8 | |
| 11 | 9 my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV]; |
| 10 | |
| 11 my $call = join " ", @ARGV[0..($#ARGV - 4)]; | |
| 1 | 12 |
| 10 | 13 system $call .' --target reads > '. $outFile and exit 1; |
| 1 | 14 |
| 15 | |
| 10 | 16 foreach(<reads*>){ |
| 1 | 17 |
| 10 | 18 my $fileType; |
| 19 | |
| 20 $fileType = $1 if /\.(\w+)$/; | |
|
12
4cbf6c6d2f2b
Fixed issue where adapter removal can not be performed and further minor issues.
jtilman
parents:
11
diff
changeset
|
21 $fileType = $format if /\.\w*fast\w$/; |
| 10 | 22 $fileType = 'tabular' if $fileType eq 'lengthdist'; |
| 23 | |
| 11 | 24 my $file = $_; |
| 25 | |
| 10 | 26 s/_//g; |
| 27 | |
| 28 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType; | |
| 29 | |
| 11 | 30 rename $file, $name; |
| 10 | 31 rename $name, $folder; |
| 1 | 32 } |
| 33 |