[Bioperl-l] sub_SeqFeature

xikun wu (IAH-C) xikun.wu at bbsrc.ac.uk
Fri Mar 9 12:41:38 EST 2007


Hi Hilmar,

Sorry for the unexpected contact!

I am using bioperl-1.4 but got problem in using "sub_SeqFeature",
nothing was returned from it. Any hints from you will be really
appreciated!

Here are the codes:

################################

use lib "/usr/local/share/bioperl-1.4";
use Bio::Seq;
use Bio::SeqIO;

die "usage: perl test.pl <embl>\n" unless @ARGV==1;
my ($embl)=@ARGV;
my $in=Bio::SeqIO->new('-file'=>$embl, '-format' => 'EMBL');
while(my $seq=$in->next_seq())
{
     my @feats=$seq->get_all_SeqFeatures();
     foreach my $feat (@feats)
     {
         if($feat->primary_tag eq "CDS")
         {
	    my ($gene_id)=$feat->each_tag_value('gene');
	    my @subfeat=$feat->sub_SeqFeature();
	    my $exon_number=scalar(@subfeat);
	    print"$gene_id\t$exon_number\t at subfeat\n";
	}
     }
}

__END__

##################################


The output is:

gene.46709      0
gene.46836      0
gene.46137      0
gene.46285      0
......


Thank you very much!

Best wishse,
Xikun

****************************
Xikun Wu
PhD in Bioinformatics
Institute for Animal Health
Compton
Nr Newbury
Berkshire, RG20 7NN
U.K.
Tel:   01635 577275
Fax:   01635 577263

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