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

Adam Witney awitney at sghms.ac.uk
Thu Jun 26 16:00:47 EDT 2003


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

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



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