[Bioperl-l] EPCR module with multiple sequence file

[Jason Stajich]

You mean you want the name of the sequence that was hit?
Do this:

When you get the feature in your loop call:
print $feat->seqname(), "\n";

If you mean that you want to see the seqname in your EMBL annotation
you'll need to explicitly add that tag to the feature like this -
NOTE: THIS SHOULD BE BEFORE YOUR $seq->add_Feature($feat) LINE.

$feat->add_tag_value('seqname',$feat->seqname());

You can also of course dump the feature a GFF by saying

print $feat->gff_string(), "\n";

See Bio::SeqFeature::Generic for the complete list of methods that are
implemented by the features which are returned from Bio::Tools::EPCR.


-jason
On Thu, 18 Jul 2002, Damien Mattei wrote:

> i have two questions about EPCR module.
>
> First is it able to parse .epcr files generated with a sequence file
> containing many fasta sequence.
>
> Second how can i retrieve the name of the sequence .
>
> if it's not clear here is how i work:
>
> e-PCR stsfile many_seq_in_one_file.nt > output.epcr
>
> and i run this program:
>
> #!/usr/bin/perl -w
> # A simple parser for ePCR data
> # assuming ePCR data is already generated in file output.epcr
>
>
> use Bio::Tools::EPCR;
> use Bio::SeqIO;
> my $parser = new Bio::Tools::EPCR(-file => 'output.epcr');
> my $seqio = new Bio::SeqIO(-format => 'fasta', -file =>
> 'many_seq_in_one_file.nt');
> my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");
>
> while( my $feat = $parser->next_feature ) {
>      # add EPCR annotation to a sequence
>      $seq->add_SeqFeature($feat);
>      print "Feature from ", $feat->start, " to ",
>      $feat->end, " Primary tag  ", $feat->primary_tag,
>      ", produced by ", $feat->source_tag(), "\n";
>
>      foreach $tag ( $feat->all_tags() ) {
> 	print "Feature has tag ", $tag, " with values, ",
> 	join(' ',$feat->each_tag_value($tag)), "\n";
>      }
>      print "new feature\n" if $feat->has_tag('new');
>      # features can have sub features
>      my @subfeat = $feat->sub_SeqFeature();
>
>      print "\n";
>
> }
>
> my $seqout = new Bio::SeqIO(-format => 'embl');
> #$seqout->write_seq($seq);
>
> this will print all the info in output.epcr
> but not the sequence name.
>
> Damien.
>
> -----------------------------
> Damien Mattei
> C.N.R.S / U.N.S.A - UMR 6549
> mailto:mattei@unice.fr
> http://www-iag.unice.fr/
> -----------------------------
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu