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comparison pyCRAC/pyBinCollector.pl @ 0:19b20927172d draft

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author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
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-1:000000000000 0:19b20927172d
1 #!/usr/bin/perl -w
2 use strict;
3 use Getopt::Long;
4
5 my %opt=(s=>"genomic",numberofbins=>20);
6
7
8 GetOptions(\%opt, "f=s","version","gtf=s","range=i","annotation=s", "numberofbins=i","min_length=i","max_length=i","s=s","o=s","ignorestrand","outputall","sd=s","ssub=s","sdel=s","asd=s","assub=s","asdel=s","out=s","options","bins1=i","bins2=i","id=s");
9
10 my $cmnd;
11
12 my $prefix = "bc_$opt{id}";
13
14 if (exists $opt{version}){
15 $cmnd = "python /usr/local/bin/pyBinCollector.py --version";
16 }
17 else{
18 $cmnd = "python /usr/local/bin/pyBinCollector.py -f $opt{f} --gtf $opt{gtf} --annotation $opt{annotation} -o $prefix";
19
20 if(exists $opt{outputall})
21 {
22 $cmnd .= " --outputall";
23 }
24
25 if(exists $opt{options}){
26
27 $cmnd .= " --range=$opt{range} --numberofbins $opt{numberofbins} --min_length $opt{min_length} --max_length $opt{max_length} -s $opt{s}";
28
29 if(exists $opt{ignorestrand}){ $cmnd .= " --ignorestrand";}
30 if(exists $opt{bins1}){ $cmnd .= " --binselect $opt{bins1} $opt{bins2}";}
31 }
32 }
33
34
35 system $cmnd;
36 if(exists $opt{outputall}){
37
38 system "mv sense_data_$prefix.txt $opt{sd}";
39 system "mv sense_subs_$prefix.txt $opt{ssub}";
40 system "mv sense_dels_$prefix.txt $opt{sdel}";
41 system "mv anti_sense_data_$prefix.txt $opt{asd}";
42 system "mv anti_sense_subs_$prefix.txt $opt{assub}";
43 system "mv anti_sense_dels_$prefix.txt $opt{asdel}";
44 }
45 else{
46 system "mv $prefix"."_cumulative_densities_$opt{annotation}"."_$opt{s}_"."$opt{numberofbins}_bins.pileup $opt{out}";
47 }