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comparison pyCRAC/pyReadCounters.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;
6
7
8 GetOptions(\%opt, "f=s","file_type=s","version","gtf=s","align_quality=i","align_score=i","range=i","length=i","max=i","distance=i","ignorestrand","overlap=i","unique","blocks","mutations=s","countoutput=s","stats=s","hittable=s","intronUTRoverlap=s","discarded=s","options","alignOpt","id=s");
9
10 my $cmnd;
11 my $prefix = "rc_$opt{id}";
12
13
14 if (exists $opt{version}){
15 $cmnd = "python /usr/local/bin/pyReadCounters.py --version";
16 }
17 else{
18 $cmnd = "python /usr/local/bin/pyReadCounters.py -f $opt{f} --file_type $opt{file_type} --gtf $opt{gtf} -o $prefix";
19
20 if(exists $opt{options}){
21
22 $cmnd .= " --range=$opt{range} --overlap=$opt{overlap}";
23
24 if(exists $opt{ignorestrand}){ $cmnd .= " --ignorestrand";}
25 }
26
27 if(exists $opt{alignOpt}){
28 $cmnd .= " --align_quality=$opt{align_quality} --align_score=$opt{align_score} --length=$opt{length} --distance=$opt{distance}";
29 if(exists $opt{max}){$cmnd .= " --max=$opt{max}";}
30 if(exists $opt{unique}){$cmnd .= " --unique";}
31 if(exists $opt{blocks}){$cmnd .= " --blocks";}
32 if(exists $opt{mutations}){$cmnd .= " --mutations=$opt{mutations}";}
33 if(exists $opt{discarded}){$cmnd .= " --discarded=$opt{discarded}";}
34
35 }
36 }
37
38
39 system $cmnd;
40 print STDOUT $cmnd;
41
42
43 if(exists $opt{blocks}){
44 system "mv $prefix"."_hittable_cDNAs.txt $opt{hittable}";
45 system "mv $prefix"."_file_statistics_cDNAs.txt $opt{stats}";
46 system "mv $prefix"."_intron_and_UTR_overlap_cDNAs.gtf $opt{intronUTRoverlap}";
47
48 if($opt{file_type} ne "gtf"){
49 system "mv $prefix"."_count_output_cDNAs.gtf $opt{countoutput}";
50 }
51 }
52 else{
53 system "mv $prefix"."_hittable_reads.txt $opt{hittable}";
54 system "mv $prefix"."_file_statistics_reads.txt $opt{stats}";
55 system "mv $prefix"."_intron_and_UTR_overlap_reads.gtf $opt{intronUTRoverlap}";
56
57 if($opt{file_type} ne "gtf"){
58 system "mv $prefix"."_count_output_reads.gtf $opt{countoutput}";
59 }
60 }