[Bioperl-l] ace to fasta conversion

Sean Crosson scrosson at uchicago.edu
Fri Jul 13 18:15:30 EDT 2007


I've been using this Bio::SeqIO script to convert EMBL and swissprot to fasta
and it works great.  We're now trying to convert a big (250 MB) .ace file to
fasta.  The documentation suggests I can do this, but everytime I run the script
below, it outputs an empty .fas file.  Does anyone have any suggestions on how
to make this script work?  Does SeqIO really convert between these file types? 
Thanks for your help.

#!/usr/bin/perl -w

use Bio::SeqIO;


$in  = Bio::SeqIO->new(-file => "454Contigs.ace",
                       -format => 'ace');
$out = Bio::SeqIO->new(-file => ">454Contigs.fas",
                       -format => 'fasta');
while ( $seq = $in->next_seq() ) {$out->write_seq($seq); }





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