[Bioperl-l] How do you pull features out of a genbank file

[Richard Adams]

Wes,
This should work:

my $seq = $seq_in->next_seq();

## now get an array of all seq features

my @fts = $seq->all_SeqFeatures;

#and array of alleles
my @allele    = grep {$_->primary_tag eq 'variation'} @fts;


for my $var (@allele) {
    print "residue ", $var->start, " has alternative nucleotide ",
($var->each_tag_value('replace'))[0], "\n";
    }
There is a good explanation of these methods in Bio::SeqFeatureI and
Bio::SeqFeature::Generic documentation

Richard



--
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk