Mercurial > repos > bioitcore > splicetrap
comparison bin/PostAnalysis @ 1:adc0f7765d85 draft
planemo upload
author | bioitcore |
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date | Thu, 07 Sep 2017 15:06:58 -0400 |
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0:d4ca551ca300 | 1:adc0f7765d85 |
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1 #!/usr/bin/perl | |
2 my $SrcFolder="/home/galaxy/galaxy-dist/tools/SpliceTrap.0.90.1/bin"; | |
3 # this script is a wrapup for Post analysis based on the ratio file output | |
4 | |
5 use strict; | |
6 use Getopt::Long; | |
7 my $RatioFile=""; | |
8 my $OutputFile = ""; | |
9 my $JunctionCut=5; | |
10 my $CutoffLevel="M"; | |
11 my $noIRM = 0; | |
12 my $noIRMstr=""; | |
13 | |
14 GetOptions ( | |
15 "i:s"=>\$RatioFile, | |
16 "o:s"=>\$OutputFile, | |
17 "c:s"=>\$CutoffLevel, | |
18 "noIRM|noirm"=>\$noIRM, | |
19 "j:i"=>\$JunctionCut | |
20 ); | |
21 | |
22 my $InputParaDes=" Usage of the script: | |
23 -i input file (.ratio file) | |
24 -o output file | |
25 -c Cutoff Level:H/[M]/L | |
26 Means High, Middle or Low | |
27 -j Junction reads per junction requirement for each exon-isoform [5] | |
28 --noIRM Use the unadjusted inclusion ratios (before IRM correction) | |
29 "; | |
30 | |
31 if($RatioFile eq "") | |
32 { | |
33 print $InputParaDes; | |
34 exit; | |
35 } | |
36 | |
37 if($CutoffLevel ne "H" and $CutoffLevel ne "M" and $CutoffLevel ne "L") | |
38 { | |
39 print $InputParaDes; | |
40 exit; | |
41 } | |
42 if($noIRM) | |
43 { | |
44 $noIRMstr= "noirm"; | |
45 } | |
46 | |
47 | |
48 system("perl $SrcFolder/ApplyCutoff.jie.pl $RatioFile $CutoffLevel $JunctionCut $noIRMstr >$OutputFile.raw"); | |
49 | |
50 open(rawfile, "$OutputFile.raw"); | |
51 open(outfile, ">$OutputFile"); | |
52 while(my $line=<rawfile>) | |
53 { | |
54 chomp($line); | |
55 my @a=split("\t",$line); | |
56 if($noIRM) | |
57 { | |
58 print outfile join("\t",$a[21],$a[1],$a[3],$a[4],$a[5],$a[6],$a[7],$a[11],$a[12],$a[13],$a[14]),"\n"; | |
59 } | |
60 else | |
61 { | |
62 print outfile join("\t",$a[21],$a[2],$a[3],$a[4],$a[5],$a[6],$a[7],$a[11],$a[12],$a[13],$a[14]),"\n"; | |
63 } | |
64 } | |
65 close(outfile); | |
66 close(rawfile); |