Filename: //bin/zff2gff3.pl

#!/usr/bin/perl use strict; use warnings; my %Feature = ( 'Exon' => 'CDS', 'Einit' => 'CDS', 'Eterm' => 'CDS', 'Esngl' => 'CDS', ); print "##gff-version 3\n"; my $seq; my %H; while (<>) { if (/^>(\S+)/) { print "#region $1\n"; $seq = $1; } else { my @f = split; if (@f == 4) { my $strand = $f[1] < $f[2] ? '+' : '-'; if ($strand eq '-') {($f[1], $f[2]) = ($f[2], $f[1])} print join("\t", $seq, 'snap', $Feature{$f[0]}, $f[1], $f[2], '.', $strand, "Name=$f[3]"), "\n"; } elsif (@f == 9) { print join("\t", $seq, 'snap', $Feature{$f[0]}, $f[1], $f[2], '.', $f[3], "Name=$f[8]"), "\n"; } else {die "input does not appear to be ZFF"} } } __END__

./Ninja\.