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