[Bioperl-l] Closing a SeqIO filehandle

[Jason Stajich]

On Mon, 27 Jan 2003, Nancy Hansen wrote:

>
> Hi!
>
> 	I can't figure out how to close the filehandle of a Bio::SeqIO
> object within my program.  I'd like to create fasta files, and then allow
> another program (called from my program) to open them.  When I do
> something simple like
>
> my $out_fasta = Bio::SeqIO->new(-file => ">$filename",
>                                 -format => 'Fasta');
> $out_fasta->write_seq($seq);
$out_fasta->close();
or
$out_fasta = undef;

This bug has been fixed in the latest bioperl.


> exec "$cm_exe $filename";
>
> The program I call doesn't see the final partial block that I suppose is
> still in the buffer.  Is there any way to flush and close the filehandle?
>
> 	Thanks,
> 	--Nancy
>
> *************************************
> Nancy F. Hansen, PhD	nhansen at nhgri.nih.gov
> Bioinformatics Group
> NIH Intramural Sequencing Center (NISC)
> 8717 Grovemont Circle, Rm. 152L
> Gaithersburg, MD 20877
> Phone: (301) 435-1560	Fax: (301) 435-6170
>
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu