issue writing to pipe with bio sequoia
Stephane Plaisance | VIB | <[email protected]> Tue, 31 May 2016 16:06:48 +0200
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Dear,
I try to bgzip my fasta outpmut fbut have an issue
my $seq_out;
if ( defined($zipit) ) {
my $bgzip = `which bgzip`;
chomp($bgzip);
die "No bgzip command available\n" unless ( $bgzip );
$seq_out = Bio::SeqIO -> newFh( -format => 'Fasta', -file => " | $bgzip -c > $outfile\.gz");
} else {
$seq_out = Bio::SeqIO -> newFh( -format => 'Fasta', -file => ">$outfile" );
}
the code fails although bgzip is in my path and the $bgzip variable sets it right
Any help is very welcome
Stephane