Mercurial > repos > fubar > jbrowse2dev
view jbrowse2/maf2bed.pl @ 6:88b9b105c09b draft
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author | fubar |
---|---|
date | Fri, 05 Jan 2024 01:58:02 +0000 |
parents | cd5d63cd0eb5 |
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#!/usr/bin/env perl use warnings; use strict; $, = ' '; $\ = "\n"; $, = "\t"; my $id = 0; my $buffer = ''; my $start = 0; my $end = 0; my $score = 0; my $chrom = ''; while (<STDIN>) { chomp; next if /^$/; my @line = split('\s+'); if (/^s\s+$ARGV[0]/) { $chrom = $line[1]; $chrom =~ s/$ARGV[0]\.//; $start = $line[2]; $end = $line[2] + $line[3]; s/^s //; s/ +/:/g; my $temp = $_; $buffer = $buffer eq '' ? $temp : "$buffer,$temp"; } elsif (/^a/) { $score = +(s/^a score=//); if($id > 0) { print $chrom, $start, $end, "$ARGV[0]_$id", $score, $buffer; } $id += 1; $buffer = ''; } elsif (/^s/) { s/^s //; s/ +/:/g; my $temp = $_; $buffer = $buffer eq '' ? $temp : "$buffer,$temp"; } } print $chrom, $start, $end, "$ARGV[0]_$id", $score, $buffer;