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comparison pyCRAC/pyBarcodeFilter.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", "b=s", "out=s", "output_path=s","id=s","m=i", "file_type=s", "both", "r=s", "version", "i");
9
10 my $cmnd;
11
12 if (exists $opt{version}){
13 $cmnd = "python /usr/local/bin/pyBarcodeFilter.py --version";
14 }
15 else{
16 $cmnd = "python /usr/local/bin/pyBarcodeFilter.py -f $opt{f} -b $opt{b} -m $opt{m} --file_type $opt{file_type}";
17
18 if(defined $opt{r}){
19
20 $cmnd.= " -r $opt{r}";
21
22 if(exists $opt{both}){
23 $cmnd .= " --both";
24 }
25 }
26
27 if(exists $opt{i}){
28 $cmnd .= " -i";
29 }
30 }
31
32 # Create the output directory (for the multiple output files)
33 my $output_path = $opt{output_path};
34
35 system $cmnd;
36
37 open(BC,$opt{b}) || die "Cannot open barcode file";
38 my %bc;
39 while(my $line = <BC>){
40 chomp($line);
41 my ($barcode,$sample) = (split(/\t/,$line))[0,1];
42 $bc{$barcode}=$sample;
43 }
44
45 system "mv barcode_statistics.txt $opt{out}";
46
47 my $ft = lc($opt{file_type});
48
49 foreach my $key(keys %bc){
50 my @split = (split(/\//,$opt{f}));
51 my $l = @split;
52 my $output = $split[$l-1];
53 $output = (split(/\./,$output))[0];
54 $output = "$output"."_"."$key"."_"."$bc{$key}"."."."$ft";
55 my $rename = "$output_path/primary_$opt{id}_$bc{$key}-1"."_visible_"."$ft";
56 system "mv $output $rename";
57
58 if(defined $opt{r}){
59 my @split2 = (split(/\//,$opt{r}));
60 $l = @split2;
61 $output = $split2[$l-1];
62 $output = (split(/\./,$output))[0];
63 $output = "$output"."_"."$key"."_"."$bc{$key}"."."."$ft";
64 $rename = "$output_path/primary_$opt{id}_$bc{$key}-2"."_visible_"."$ft";
65 system "mv $output $rename";
66 }
67 }
68
69
70 close BC;
71