[Bioperl-l] write_seq 2 variable?

[Marc Logghe]

use Bio::SeqIO;
use IO::String;

my $s;
my $io = IO::String->new($s);
my $out = Bio::SeqIO->new(-fh => $io, -format => 'fasta');
$out->write_seq($seq);

In that way your fasta sequence output ends up in the variable $s.
HTH,
Marc

> -----Original Message-----
> From: michael [mailto:michael@galton.ucl.ac.uk] 
> Sent: Tuesday, September 10, 2002 11:20 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] write_seq 2 variable?
> 
> 
> 
> 
> 	The 4 line sequence formatters using SeqIO are 
> wonderful however,  I'd like to save the output of 
> write_seq() into a variable for a bit of extra processing.
> 	How do I do that?
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Michael John Lush PhD		 	 Tel:44-20-7679-5027
> Nomenclature Bioinformatics Support 	 Fax:44-20-7387-3496
> HUGO Gene Nomenclature Committee Email:  
> nome@galton.ucl.ac.uk The Galton Laboratory University 
> College London, UK
> URL: http://www.gene.ucl.ac.uk/nomenclature/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
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