[Bioperl-l] issue writing to pipe with bio sequoia

[Stephane Plaisance | VIB |]

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