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

[Brian Osborne]

Heikki,

I'll do these 3 things.

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 Heikki
Lehvaslaiho
Sent: Friday, June 27, 2003 5:28 AM
To: Jason Stajich; Brian Osborne
Cc: Adam Witney; bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] Generating multiple fasta files from an embl file


Brian,

Could you take care of porting the current FAQ from head into 1.2
branch, please.

Also, if you have time, this $cds_feature->spliced_seq() should be in
the FAQ, too. It might be good idea to rephrase Q5.3 and Q5.4 and put
spliced_seq() into a new Q5.5.

Let me know, if you can not do it,

        -Heikki



On Thu, 2003-06-26 at 17:57, Jason Stajich wrote:
> This should get you what you want:
>   my $geneseq = $cds_feature->spliced_seq();
>
> -jason
> On Thu, 26 Jun 2003, Adam Witney wrote:
>
> > 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
> >
> >
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
--
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

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