[Omaha.pm] BioPerl: Nucleic acids
Jay Hannah
jay at jays.net
Fri Feb 29 11:45:35 PST 2008
Just another little demo...
Read a GenBank file and print all the NA sequences which compose CDSs.
#!/usr/bin/perl
use strict;
use Bio::SeqIO;
my $io = Bio::SeqIO->new( -format => 'genbank',
-file => 'AP008934.gbk');
my $seq;
while ( $seq = $io->next_seq() ) {
foreach my $feat ( $seq->get_SeqFeatures ) {
next unless ($feat->primary_tag eq "CDS");
print $feat->spliced_seq->seq, "\n";
}
}
spliced_seq is an amazing, magical beast. :)
References:
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
http://www.bioperl.org/wiki/HOWTO:SeqIO
Cheers,
j
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