[Bioperl-l] Translate to 6 ORF's
Wiepert, Mathieu
Wiepert.Mathieu@mayo.edu
Tue, 23 Oct 2001 10:33:16 -0500
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);
}