[Bioperl-l] Generating multiple fasta files from an embl file

[Brian Osborne]

Adam,

I'm not sure I understand the question exactly but it may be that you want
to examine the LocationI object, which you can get by:

$locobj = $feat->location

With that in hand you'll be able to iterate over each location using
each_Location(). You can select the Location object you want and attach it
to the Seq object in question. FAQ question 5.4 shows an example of
something like this.

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Adam Witney
Sent: Thursday, June 26, 2003 10:01 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Generating multiple fasta files from an embl file

Hi,

I am passing an embl file and generating a multiple fasta file of the genes.
In the embl file there are entries like this

FT   CDS             complement(join(104291..105577,107535..108365))

The two joined pieces of DNA actually span two other genes (insertion
elements)

I am passing the file like so:

......
my $embl_obj = Bio::SeqIO->new('-file' => "$embl_file",
                              '-format' => 'embl');

while (my $seq = $embl_obj->next_seq())  # gets the genome sequence object
  {
   my @features = $seq->all_SeqFeatures;

   foreach my $feat (@features)         # gets the genes
     {
      if($feat->primary_tag eq 'CDS')
         {
          my $seq_obj = $feat->seq;

          $seq = $seq_obj->seq;
......

However the $seq variable now contains the whole piece of DNA from
104291-108365 ie including the two insertion elements.

What I would like is to get the two joined fragments separately... Is there
a way to do this with bioperl? Or a better way of doing the whole process
here?

Thanks

Adam


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