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

[Roy Chaudhuri]

Hi Stephane,

According to the SeqIO docs your way should work, so this is probably a 
bug. However, Bio::SeqIO can accept a filehandle instead using the -fh 
option, so as a workaround you could try something like this:

open my $fh, '|$bgzip -c > $outfile.gz' or die $!;
$seq_out=Bio::SeqIO->newFh(-format=>'fasta', -fh=>$fh);

Cheers,
Roy.

On 31/05/2016 15:06, Stephane Plaisance | VIB | wrote:
> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>