[Bioperl-l] ace to fasta conversion
Joel Martin
j_martin at lbl.gov
Sat Jul 14 00:05:45 UTC 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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