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view scripts/get_class.pl @ 0:28d1a6f8143f draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author | portiahollyoak |
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date | Mon, 25 Apr 2016 13:08:56 -0400 |
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#!/share/bin/perl # chr2L 19384 20049 FBgn0001283_jockey wXh24,-1;harwich,-8,+5;whXw21,-4,+1;whXw14,-5;wXh14,+2; +- sense chr2L:19562.19645 my @sample=("$ARGV[1]"); print "chr\tstart\tend\ttransposonName\tstrand\ttransposonStrand\tbreak\tclass"; print "\t$_\_class\t$_\_plus\t$_\_minus" foreach @sample; print "\n"; open in,$ARGV[0]; while(<in>) { chomp; my($chrom,$start,$end,$transposonName,$class,$strand,$transposonStrand,$break)=split/\t/; my %classCounts; my ($tcplus,$tcminus)=(0,0); foreach $s (split/;/,$class) { my ($name,@counts)=split/,/,$s; foreach my $c (@counts) { my $strand=($c>0)?"+":"-"; $classCounts{$name}{$strand}=$c; $tcplus+=$c if $c>0; $tcminus+=$c if $c<0; } } print "$chrom\t$start\t$end\t$transposonName\t$strand\t$transposonStrand\t$break"; print "\t1p1" if $tcplus>0 && $tcminus<0; print "\t2p" if ($tcplus>1 && $tcminus==0) || ($tcplus==0 && $tcminus<-1); print "\tsingleton" if ($tcplus<=1 && $tcminus==0 && $tcplus>0) || ($tcplus==0 && $tcminus>=-1 && $tcminus<0); print "\tNone" if ($tcminus==0 && $tcplus==0); foreach my $s (@sample) { $classCounts{$s}{"+"}=0 if not exists $classCounts{$s}{"+"}; $classCounts{$s}{"-"}=0 if not exists $classCounts{$s}{"-"}; print "\t1p1" if $classCounts{$s}{"+"}>0 && $classCounts{$s}{"-"}<0; print "\t2p" if ($classCounts{$s}{"+"}>1 && $classCounts{$s}{"-"}==0) || ($classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}<-1); print "\tsingleton" if ($classCounts{$s}{"+"}<=1 && $classCounts{$s}{"-"}==0 && $classCounts{$s}{"+"}>0) || ($classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}>=-1 && $classCounts{$s}{"-"}<0); print "\tNone" if $classCounts{$s}{"+"}==0 && $classCounts{$s}{"-"}==0; print "\t",$classCounts{$s}{"+"},"\t",$classCounts{$s}{"-"}; } print "\n"; } close in;