[Bioperl-l] Translate to 6 ORF's

[Wiepert, Mathieu]

Wow, thanks...

 -----Original Message-----
From: 	Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk] 
Sent:	Thursday, October 25, 2001 11:05 AM
To:	Wiepert, Mathieu; Bioperl
Subject:	Re: [Bioperl-l] Translate to 6 ORF's


I decided that translations in 3 forward or in all 6 frames is common enough
request to have them in bioperl. To not change sequence interfaces, I added
the two methods into Bio::SeqUtils.

 #takes the same arguments as translate (frame naturally ignored)
 @seqs = Bio::SeqUtils->translate_6frames($seq);

	-Heikki

"Wiepert, Mathieu" wrote:
> 
> I want to translate a large fasta file with many sequences to proteins in
> all 6 ORF's.  The code is simple, copied from the docs somewhere.  Do I
have
> to reverse the sequence and then translate to get the three reverse ORF's?
> 
> use Bio::SeqIO;
> 
> $in  = Bio::SeqIO->new(-file => "file1.fa" , '-format' => 'Fasta');
> $out = Bio::SeqIO->new(-file => ">file1_t1.fa" , '-format' => 'Fasta');
> 
>     while ( my $seq = $in->next_seq() ) {
>         $translation = $seq->translate(undef,undef,0);
>         $out->write_seq($translation);
>     }
> 
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