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#!/usr/bin/perl |
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use strict; |
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#use Getopt::Std; |
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#use FindBin;use lib $FindBin::Bin; |
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|
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my $usage = q/Usage: |
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jigsaw2itt.pl <input_jigsaw_gff> <output_iit_file> |
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|
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/; |
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umask 0002; |
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my ($infile, $outfile) = @ARGV; |
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die("$usage\nOutput file name required!\n") unless $outfile; |
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|
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my $inh; |
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|
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if ($infile eq '-') { |
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$inh=\*STDIN; |
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} |
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else { |
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open(INFILE, $infile) || die("Error opening input file $infile!\n"); |
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$inh=\*INFILE; |
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} |
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|
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my $curmodel; #current model name |
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my $curtag; #chromosome and strand for current model |
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my @exd; #exons for current model |
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|
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open(TOIIT, '| iit_store -o '.$outfile) |
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|| die("Error opening pipe to iit_store ($!)!\n"); |
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while (<$inh>) { |
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next if m/^\s*#/; |
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chomp; |
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my ($chr, $jsver, $exontype, $exonstart, $exonend, $jscore, |
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$strand, $frame, $lnum)=split(/\t/); |
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next unless $lnum>0; |
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($exonstart, $exonend)=($exonend, $exonstart) if $exonend<$exonstart; |
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my $locus=$chr.'.jsm.'.$lnum; |
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if ($locus ne $curmodel) { |
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&writeModel() if $curmodel; |
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$curmodel=$locus; |
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$curtag=$chr.$strand; |
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@exd=([$exonstart, $exonend]); |
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next; |
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} |
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push(@exd, [$exonstart, $exonend]); |
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} |
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|
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writeModel() if $curmodel; |
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|
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close(INFILE) unless $infile eq '-'; |
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close(TOIIT); |
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|
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sub writeModel { |
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my @ex= sort { $main::a->[0] <=> $main::b->[0] } @exd; |
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my ($mstart, $mend)=($ex[0]->[0], $ex[-1]->[1]); |
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my @exw = map { $_->[0].'-'.$_->[1] } @ex; |
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print TOIIT ">$curmodel $mstart $mend $curtag\n"; |
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print TOIIT join(',',@exw)."\n"; |
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} |
