diff maf2bed.pl @ 0:d78175596286 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maf2bed.pl	Mon Jan 08 09:20:33 2024 +0000
@@ -0,0 +1,46 @@
+#!/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;