[Bioperl-l] Creating and retrieving seqfeatures by name

[Chad Matsalla]

Hi All,

I would like to create SeqFeatures and retrieve them by name.

Here is some example code:

my $seq = new Bio::Seq( -seq =>
	'atatatatatatatatatatatatatatatatatatatataaatatatatatatatatatata',
	-primary_id => 'Chad1');
my $feature = new Bio::SeqFeature::Generic( -start => '10',
					-end => '20');
$feature->attach_seq(
               new Bio::PrimarySeq(-seq => $sequence,
                                   -display_id => "Chads_kewl_feature")
);
$seq->add_SeqFeature($feature);


So, now how can I get the sequence for "Chads_kewl_feature", by name,
from $seq?

This is what I want:

my $chads_sequence = $seq->get_feature_sequence(-feature_name =>
'Chads_kewl_feature");

_or even better_

my $feature = $seq->get_feature_by_name(-name=>'Chads_kewl_feature');

This is what I was doing:
my @features = $seq->all_SeqFeatures();
foreach (@features) {
	if ($_->seqname() eq "Chads_kewl_feature") {
		print("Chads_kewl_feature's sequence is:\n");
     		print("\t ".$_->entire_seq()->seq()."\n");
	}
}

Thanks for your help,

Chad Matsalla



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