Mercurial > repos > swebb > pycrac
comparison pyCRAC/pyFastqDuplicateRemover.pl @ 0:19b20927172d draft
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| author | swebb |
|---|---|
| date | Tue, 18 Jun 2013 09:11:00 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:19b20927172d |
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| 1 #!/usr/bin/perl -w | |
| 2 use strict; | |
| 3 use Getopt::Long; | |
| 4 | |
| 5 my %opt; | |
| 6 | |
| 7 | |
| 8 GetOptions(\%opt, "f=s", "r=s", "o=s", "out2=s", "version","id=s"); | |
| 9 | |
| 10 my $cmnd; | |
| 11 | |
| 12 if (exists $opt{version}){ | |
| 13 $cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py --version"; | |
| 14 } | |
| 15 else{ | |
| 16 $cmnd = "python /usr/local/bin/pyFastqDuplicateRemover.py -f $opt{f} -o $opt{id}"; | |
| 17 | |
| 18 if(defined $opt{r}){ | |
| 19 $cmnd.= " -r $opt{r}"; | |
| 20 } | |
| 21 } | |
| 22 | |
| 23 system $cmnd; | |
| 24 | |
| 25 | |
| 26 | |
| 27 if(defined $opt{r}){ | |
| 28 system "mv $opt{id}"."_1.fasta $opt{o}"; | |
| 29 system "mv $opt{id}"."_2.fasta $opt{out2}"; | |
| 30 } | |
| 31 else{ | |
| 32 system "mv $opt{id} $opt{o}"; | |
| 33 } | |
| 34 |