Mercurial > repos > morinlab > calc_cnsegments

annotate calc_cnsegements_titan.pl @ 0:c6e48c6ac606 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:16:32 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
1 #!/usr/bin/perl -w
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
2 =head1 NAME
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
3
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
4 createTITANsegmentfiles.pl
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
5
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
6 -head1 SYNOPSIS
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
7
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
8 =head1 OPTIONS
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
9 -id <string>
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
10 -outfile|o <string>
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
11 -symmetric|s <boolean> {1 - true; 0 - false}; Default: 1
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
12 -outIGV|igv <string> Required:
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
13 -infile|i <string> Required: TITAN *titan.txt file
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
14
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
15 =head1 DESCRIPTION
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
16
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
17 =head1 CONTACT
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
18
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
19 Gavin Ha <gha@bccrc.ca>
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
20
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
21 =cut
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
22
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
23 use strict;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
24 use List::Util qw[min max];
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
25 use File::Basename;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
26 use Getopt::Long;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
27
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
28
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
29 my $version = '0.1.3';
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
30
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
31 sub usage () {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
32 exec('perldoc', $0);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
33 exit;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
34 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
35
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
36 my ($id, $outfile, $symmetric, $outIGV, $infile, $calls, $help);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
37 $id=0;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
38 $calls = 1;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
39 $symmetric = 1;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
40 GetOptions (
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
41 'id=s' => \$id,
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
42 'infile|i=s' => \$infile,
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
43 'symmetric|s=i' => \$symmetric,
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
44 'outfile|o=s' => \$outfile,
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
45 'outIGV|igv=s' => \$outIGV,
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
46 'help|?' => \$help
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
47 );
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
48
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
49 if($help) {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
50 &usage();
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
51 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
52 print "Parameters:\nid=$id\ninfile=$infile\noutfile=$outfile\noutIGV=$outIGV\n";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
53
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
54 my ($name,$path,$suffix) = fileparse($infile);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
55 #my @jnk;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
56 #($id,@jnk) = split(/\_/,$name) if ~defined($id);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
57 my $nameOut = $id;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
58
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
59 open OUTFILE, ">$outfile" || die("Cannot write to $outfile\n");
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
60 open IGV, ">$outIGV" || die("Cannot write to $outIGV\n");
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
61 print OUTFILE "Sample\tChromosome\tStart_Position(bp)\tEnd_Position(bp)\tLength(bp)\tMedian_Ratio\tMedian_logR\tTITAN_state\tTITAN_call\tCopy_Number\tMinorCN\tMajorCN\tClonal_Cluster\tClonal_Frequency\n";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
62 print IGV "sample\tchr\tstart\tend\tnum.mark\tmedian\n";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
63 open(SEGFILE, $infile) || die("Can't open $infile!\n");
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
64 my $header = <SEGFILE>;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
65 my $line = <SEGFILE>; chomp($line);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
66 my($chr, $start, $ref, $nRef, $N, $ratio, $logR, $cn, $state, $call, $clust, $clustFreq, @rest) = split(/\t/,$line);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
67 my $end = $start;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
68 my @totalRatio=();
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
69 my @totalLogR=();
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
70 push(@totalRatio,max($ratio,1-$ratio));
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
71 push(@totalLogR,$logR);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
72 while($line=<SEGFILE>) {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
73 chomp($line);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
74 my ($chrS, $startS, $refS, $nRefS, $NS, $ratioS, $logRS, $cnS, $stateS, $callS, $clustS, $clustFreqS, @rest) = split(/\t/,$line);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
75 if ($chrS ne $chr || $callS ne $call || $clustS ne $clust){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
76 my $medianRatio = max($ratio,1-$ratio); #1 position only
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
77 my $medianLogR = $logR;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
78 $medianRatio = median(@totalRatio) if (($end-$start+1)>1); #more than 1 position
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
79 $medianLogR = median(@totalLogR) if (($end-$start+1)>1);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
80 my @majmin;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
81 if ($symmetric == 0){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
82 @majmin = &getMinorMajorCN($state);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
83 }elsif ($symmetric == 1){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
84 @majmin = &getMinorMajorCNSymmetric($state);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
85 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
86 my $output = $nameOut . "\t" . $chr . "\t" . $start . "\t" . $end . "\t" . ($end-$start+1). "\t" . sprintf("%.2f",$medianRatio) . "\t" . sprintf("%.2f",$medianLogR);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
87 $output = $output . "\t" . $state . "\t" . $call if ($calls);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
88 $output = $output . "\t" . $cn . "\t" . $majmin[0] . "\t" . $majmin[1] . "\t" . $clust . "\t" . $clustFreq;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
89 print OUTFILE $output . "\n";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
90 my $output2 = $nameOut . "\t" . $chr . "\t" . $start . "\t" . $end . "\t" . scalar(@totalRatio). "\t" . sprintf("%.2f",$medianLogR);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
91 print IGV $output2 . "\n";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
92 #reset
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
93 @totalRatio = ();
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
94 @totalLogR = ();
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
95 $start = $startS;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
96 }else{
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
97
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
98 #push(@totalRatio,max($ratioS,1-$ratioS));
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
99 #assign current state to previous variables
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
100 #new end, but start still the same
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
101 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
102 ($chr, $end, $ref, $nRef, $N, $ratio, $logR, $cn, $state, $call, $clust, $clustFreq) = ($chrS, $startS, $refS, $nRefS, $NS, $ratioS, $logRS, $cnS, $stateS, $callS, $clustS, $clustFreqS);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
103 push(@totalRatio,max($ratioS,1-$ratioS));
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
104 push(@totalLogR,$logRS);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
105 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
106
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
107 #final output
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
108 my $medianRatio = max($ratio,1-$ratio); #1 position only
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
109 $medianRatio = median(@totalRatio) if (($end-$start+1)>1); #more than 1 position
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
110 my $medianLogR = $logR;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
111 $medianLogR = median(@totalLogR) if (($end-$start+1)>1);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
112 my $output = $nameOut . "\t" . $chr . "\t" . $start . "\t" . $end . "\t" . ($end-$start+1). "\t" . sprintf("%.4f",$medianRatio) . "\t" . sprintf("%.2f",$medianLogR);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
113 my @majmin;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
114 if ($symmetric == 0){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
115 @majmin = &getMinorMajorCN($state);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
116 }elsif ($symmetric == 1){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
117 @majmin = &getMinorMajorCNSymmetric($state);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
118 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
119 $output = $output . "\t" . $state . "\t" . $call if ($calls);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
120 $output = $output . "\t" . $cn . "\t" . $majmin[0] . "\t" . $majmin[1] . "\t" . $clust . "\t" . $clustFreq;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
121 print OUTFILE $output . "\n";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
122 my $output2 = $nameOut . "\t" . $chr . "\t" . $start . "\t" . $end . "\t" . scalar(@totalRatio). "\t" . sprintf("%.2f",$medianLogR);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
123 print IGV $output2 . "\n";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
124 close OUTFILE;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
125 close IGV;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
126 #my $returnCode = `sort -k2,2n -k3,3n $outfile\.tmp > $outfile; rm $outfile\.tmp;`;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
127 close SEGFILE;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
128
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
129
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
130 sub median {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
131 my (@array_ref) = @_;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
132 my $count = scalar @array_ref;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
133 # Sort a COPY of the array, leaving the original untouched
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
134 my @array = sort { $a <=> $b } @array_ref;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
135 if ($count % 2) {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
136 return $array[int($count/2)];
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
137 } else {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
138 return ($array[$count/2] + $array[$count/2 - 1]) / 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
139 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
140 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
141
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
142
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
143 sub getMinorMajorCN {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
144 my ($state) = @_;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
145 my @majmin; $majmin[0]="NA"; $majmin[1]="NA";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
146 if ($state==0){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
147 $majmin[0] = 0; $majmin[1] = 0;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
148 }elsif ($state==1 || $state==2){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
149 $majmin[0] = 0; $majmin[1] = 1;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
150 }elsif($state==4){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
151 $majmin[0] = 1; $majmin[1] = 1;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
152 }elsif ($state==3 || $state==5){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
153 $majmin[0] = 0; $majmin[1] = 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
154 }elsif ($state==6 || $state==9){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
155 $majmin[0] = 0; $majmin[1] = 3;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
156 }elsif ($state==10 || $state==14){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
157 $majmin[0] = 0; $majmin[1] = 4;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
158 }elsif ($state==15 || $state==20){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
159 $majmin[0] = 0; $majmin[1] = 5;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
160 }elsif ($state==7 || $state==8){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
161 $majmin[0] = 1; $majmin[1] = 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
162 }elsif ($state==11 || $state==13){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
163 $majmin[0] = 1; $majmin[1] = 3;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
164 }elsif ($state==16 || $state==19){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
165 $majmin[0] = 1; $majmin[1] = 4;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
166 }elsif ($state==17 || $state==18){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
167 $majmin[0] = 2; $majmin[1] = 3;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
168 }elsif ($state==12){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
169 $majmin[0] = 2; $majmin[1] = 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
170 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
171 #my $retVal = ($majmin[0],$majmin[1]);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
172 return @majmin;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
173 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
174
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
175 sub getMinorMajorCNSymmetric {
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
176 my ($state) = @_;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
177 my @majmin; $majmin[0]="NA"; $majmin[1]="NA";
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
178 if ($state==0){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
179 $majmin[0] = 0; $majmin[1] = 0;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
180 }elsif ($state==1){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
181 $majmin[0] = 0; $majmin[1] = 1;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
182 }elsif($state==2){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
183 $majmin[0] = 0; $majmin[1] = 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
184 }elsif ($state==3){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
185 $majmin[0] = 1; $majmin[1] = 1;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
186 }elsif ($state==4){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
187 $majmin[0] = 0; $majmin[1] = 3;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
188 }elsif ($state==5){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
189 $majmin[0] = 1; $majmin[1] = 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
190 }elsif ($state==6){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
191 $majmin[0] = 0; $majmin[1] = 4;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
192 }elsif ($state==7){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
193 $majmin[0] = 1; $majmin[1] = 3;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
194 }elsif ($state==8){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
195 $majmin[0] = 2; $majmin[1] = 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
196 }elsif ($state==9){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
197 $majmin[0] = 0; $majmin[1] = 5;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
198 }elsif ($state==10){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
199 $majmin[0] = 1; $majmin[1] = 4;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
200 }elsif ($state==11){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
201 $majmin[0] = 2; $majmin[1] = 3;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
202 }elsif ($state==12){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
203 $majmin[0] = 0; $majmin[1] = 6;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
204 }elsif ($state==13){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
205 $majmin[0] = 1; $majmin[1] = 5;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
206 }elsif ($state==14){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
207 $majmin[0] = 2; $majmin[1] = 4;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
208 }elsif ($state==15){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
209 $majmin[0] = 3; $majmin[1] = 3;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
210 }elsif ($state==16){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
211 $majmin[0] = 0; $majmin[1] = 7;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
212 }elsif ($state==17){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
213 $majmin[0] = 1; $majmin[1] = 6;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
214 }elsif ($state==18){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
215 $majmin[0] = 2; $majmin[1] = 5;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
216 }elsif ($state==19){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
217 $majmin[0] = 3; $majmin[1] = 4;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
218 }elsif ($state==20){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
219 $majmin[0] = 0; $majmin[1] = 8;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
220 }elsif ($state==21){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
221 $majmin[0] = 1; $majmin[1] = 7;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
222 }elsif ($state==22){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
223 $majmin[0] = 2; $majmin[1] = 6;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
224 }elsif ($state==23){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
225 $majmin[0] = 3; $majmin[1] = 5;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
226 }elsif ($state==24){
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
227 $majmin[0] = 4; $majmin[1] = 4;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
228 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
229 #my $retVal = ($majmin[0],$majmin[1]);
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
230 return @majmin;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
231 }
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
232
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
233
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
234 #Read more: http://wiki.answers.com/Q/How_can_you_calculate_the_average_and_median_in_perl_by_subroutine#ixzz1LcMWdXEE
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
235 #sub median{
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
236 # my @a = sort @_;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
237 # return ($a[$#a/2] + $a[@a/2]) / 2;
c6e48c6ac606 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
parents:
diff changeset
238 #}