Mercurial > repos > swebb > pycrac
comparison pyCRAC/pyGTF2bedGraph.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, "gtf=s","po=s","version","mo=s","count=i","chromfile=s","t=s","iCLIP","track","name=s","description=s","color=s","s=s","id=s"); | |
| 9 | |
| 10 my $cmnd; | |
| 11 my $prefix = "gb_$opt{id}"; | |
| 12 $prefix =~ s/\s/_/g; | |
| 13 | |
| 14 | |
| 15 if (exists $opt{version}){ | |
| 16 $cmnd = "python /usr/local/bin/pyGTF2bedGraph.py --version"; | |
| 17 } | |
| 18 else{ | |
| 19 $cmnd = "python /usr/local/bin/pyGTF2bedGraph.py --gtf $opt{gtf} --chromfile $opt{chromfile} -t $opt{t} --count $opt{count} -o $prefix"; | |
| 20 | |
| 21 if(exists $opt{iCLIP}){ | |
| 22 | |
| 23 $cmnd .= " --iCLIP"; | |
| 24 } | |
| 25 | |
| 26 if(exists $opt{track}){ | |
| 27 $cmnd .= " --track --name \"$opt{name}\" --description \"$opt{description}\""; | |
| 28 | |
| 29 if(exists $opt{color}){$cmnd .= " --color $opt{color}";} | |
| 30 if(exists $opt{s}){$cmnd .= " -s \"$opt{s}\"";} | |
| 31 } | |
| 32 } | |
| 33 | |
| 34 system $cmnd; | |
| 35 | |
| 36 system "mv $prefix"."_plus_strand.bedgraph $opt{po}"; | |
| 37 system "mv $prefix"."_minus_strand.bedgraph $opt{mo}"; | |
| 38 |