/usr/bin/zff2gff3.pl is in snap 2013-11-29-6.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | #!/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__
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