[Bioperl-l] ace to fasta conversion

Joel Martin j_martin at lbl.gov
Fri Jul 13 20:05:45 EDT 2007


Hello,
	the SeqIO 'ace' is an AceDB file, the 454*ace you are trying to use
is a phrap/consed ace file.  They aren't related at all. You might try poking
around in Bio::AssemblyIO which should read assembly ace files.

Joel

On Fri, Jul 13, 2007 at 10:15:30PM +0000, Sean Crosson wrote:
> 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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