Mercurial > repos > portiahollyoak > temp
comparison scripts/get_class.pl @ 0:28d1a6f8143f draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author | portiahollyoak |
---|---|
date | Mon, 25 Apr 2016 13:08:56 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:28d1a6f8143f |
---|---|
1 #!/share/bin/perl | |
2 | |
3 # chr2L 19384 20049 FBgn0001283_jockey wXh24,-1;harwich,-8,+5;whXw21,-4,+1;whXw14,-5;wXh14,+2; +- sense chr2L:19562.19645 | |
4 | |
5 my @sample=("$ARGV[1]"); | |
6 | |
7 print "chr\tstart\tend\ttransposonName\tstrand\ttransposonStrand\tbreak\tclass"; | |
8 print "\t$_\_class\t$_\_plus\t$_\_minus" foreach @sample; | |
9 print "\n"; | |
10 open in,$ARGV[0]; | |
11 while(<in>) | |
12 { | |
13 chomp; | |
14 my($chrom,$start,$end,$transposonName,$class,$strand,$transposonStrand,$break)=split/\t/; | |
15 my %classCounts; | |
16 my ($tcplus,$tcminus)=(0,0); | |
17 foreach $s (split/;/,$class) | |
18 { | |
19 my ($name,@counts)=split/,/,$s; | |
20 foreach my $c (@counts) | |
21 { | |
22 my $strand=($c>0)?"+":"-"; | |
23 $classCounts{$name}{$strand}=$c; | |
24 $tcplus+=$c if $c>0; | |
25 $tcminus+=$c if $c<0; | |
26 } | |
27 } | |
28 print "$chrom\t$start\t$end\t$transposonName\t$strand\t$transposonStrand\t$break"; | |
29 print "\t1p1" if $tcplus>0 && $tcminus<0; | |
30 print "\t2p" if ($tcplus>1 && $tcminus==0) || ($tcplus==0 && $tcminus<-1); | |
31 print "\tsingleton" if ($tcplus<=1 && $tcminus==0 && $tcplus>0) || ($tcplus==0 && $tcminus>=-1 && $tcminus<0); | |
32 print "\tNone" if ($tcminus==0 && $tcplus==0); | |
33 foreach my $s (@sample) | |
34 { | |
35 $classCounts{$s}{"+"}=0 if not exists $classCounts{$s}{"+"}; | |
36 $classCounts{$s}{"-"}=0 if not exists $classCounts{$s}{"-"}; | |
37 print "\t1p1" if $classCounts{$s}{"+"}>0 && $classCounts{$s}{"-"}<0; | |
38 print "\t2p" if ($classCounts{$s}{"+"}>1 && $classCounts{$s}{"-"}==0) || ($classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}<-1); | |
39 print "\tsingleton" if ($classCounts{$s}{"+"}<=1 && $classCounts{$s}{"-"}==0 && $classCounts{$s}{"+"}>0) || ($classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}>=-1 && $classCounts{$s}{"-"}<0); | |
40 print "\tNone" if $classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}==0; | |
41 print "\t",$classCounts{$s}{"+"},"\t",$classCounts{$s}{"-"}; | |
42 } | |
43 print "\n"; | |
44 } | |
45 close in; |