[Bioperl-l] clone ID to Accession ID genbank

[Irisbuiton at gmail.com]

Many thanks!

Such a stupid mistake...

IRis.

On Feb 4, 2010 9:15am, "Cook, Malcolm" <MEC at stowers.org> wrote:
> remove the -reldate



> Malcolm Cook

> Stowers Institute for Medical Research - Bioinformatics

> Kansas City, Missouri USA







> > -----Original Message-----

> > From: bioperl-l-bounces at lists.open-bio.org

> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Iris Buiton

> > Sent: Thursday, February 04, 2010 10:06 AM

> > To: bioperl-l at bioperl.org

> > Subject: [Bioperl-l] clone ID to Accession ID genbank

> >

> > Hi members of Bioperl,

> >

> > I am trying to run some code that given a clone ID (for instance,

> > CH255-149A8) get the accesion ID (AC238489.2).

> >

> > The problem is that using this ID, it works perfectly, but

> > using this other ID (CH251-558O8) I do not get anything (not

> > $seq object is obtained). Checking to Genbank, this clone

> > exist, there is seqeunce, and the accession ID should be AC147515.1

> >

> > This is the code:

> >

> > my $name_file="CH251-558O8";

> >

> > my $query = Bio::DB::Query::GenBank->new

> > (-query => $name_file,

> > -reldate => '30',

> > -db => 'nucleotide');

> > #eval 'my $seqio = $gb->get_Stream_by_query($query)';

> > print $query->count,"\n";

> >

> >

> > my $gb = Bio::DB::GenBank->new();

> >

> > my $seqio = $gb->get_Stream_by_query($query);

> >

> > print "Running $name_file.....\n";

> >

> >

> > while( my $seq = $seqio->next_seq ) {

> > if ($seq->accession_number)

> > {

> > print "$name_file = ", $seq->accession_number," = ", $seq-

> > >length,"\n" ;

> > }else

> > {

> > print "$name_file = #N/A \n" ;

> > }

> > }

> >

> > Any ideas what am I doing wrong?

> >

> > Thanks!

> >

> > Iris

> > _______________________________________________

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> > Bioperl-l at lists.open-bio.org

> > http://lists.open-bio.org/mailman/listinfo/bioperl-l

> >