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

[Mark A Jensen]

Awesome Roy, thanks !

On Tue, May 31, 2016 at 11:39 AM, Roy Chaudhuri < roy.chaudhuri at gmail.com 
[roy.chaudhuri at gmail.com] > wrote:
Hi Stephane,

Please remember to copy in the mailing list on replies. In my tests, a
leading space doesn't make any difference to the issue - Bio::SeqIO
still tries to read from the pipe rather than writing to it.

Mark - I have opened an issue on github:
https://github.com/bioperl/bioperl-live/issues/153

I think the issue is the regex in Bio::Root::IO->cleanfile not
recognising a leading pipe character as indicating a "write" filehandle.

Cheers,
Roy.

On 31/05/2016 15:58, Stephane Plaisance | VIB | wrote:
 > Thanks a lot Roy,
 >
 > I found that a leading space before the pipe and possibly the space 
directly after it were guilty, leading to the executable not found although 
fully provided with path ??? what works is
 >>> -file => " |$bgzip -c > $outfile\.gz")
 >
 > but you fh version is precious and I will record it for future use.
 >
 > Thanks!
 > stephane
 >
 >> On 31 May 2016, at 16:45, Roy Chaudhuri <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
 >>>
 >
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20160531/b2887d3d/attachment.html>