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

[Mark A Jensen]

Stephane, Roy
Can we open issue at github, bioperl-live ?
Mark

On Tue, May 31, 2016 at 10:53 AM, Roy Chaudhuri < roy.chaudhuri at gmail.com 
[roy.chaudhuri at gmail.com] > wrote:
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
 >
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