[Bioperl-l] Problem retrieving CDS by Acession #

Chris Fields cjfields at uiuc.edu
Thu Sep 7 15:04:50 EDT 2006


...
> > If you know that you want the most recent version, just strip
> > the version
> > information and use get_Seq_by_acc().
> >
> > Sean
> >
> 
> 
> Sorry, maybe I'm not being clear.  Suppose I only had the accession #,
> XM_547879.  If I call get_Seq_by_acc('XM_547879'), it gives the warning
> above.  That shouldn't be because I'm giving a valid accession number.
> I suspect something is wrong in the parsing of whatever NCBI is
> returning.

You might try updating your local Bioperl; I can retrieve it using
bioperl-live:

---------------------

use Bio::DB::GenBank;
use Bio::SeqIO;

my $fac = Bio::DB::GenBank->new();
my $seq = $fac->get_Seq_by_acc('XM_547879');
my $seqout = Bio::SeqIO->new(-fh    => \*STDOUT,
                             -format => 'genbank');
$seqout->write_seq($seq);
---------------------

Gets this sequence (truncated for brevity):

---------------------
LOCUS       XM_547879               1056 bp    mRNA    linear   MAM
30-AUG-2005
DEFINITION  PREDICTED: Canis familiaris similar to Synaptojanin 2 binding
            protein (Mitochondrial outer membrane protein 25) (LOC490757),
            mRNA.
ACCESSION   XM_547879
VERSION     XM_547879.2  GI:73964245
KEYWORDS    .
SOURCE      Canis familiaris (dog).
  ORGANISM  Canis familiaris
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi;
            Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia;
            Canidae; Canis.
....
---------------------

Chris




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