[Bioperl-l] Get variation included in genbank file

[Jessica Sun]

Great ! Yet, how do you add this SNP as an Feature tag named as Variation
into the gbk file format automatically?

thx


On Thu, Jun 10, 2010 at 4:11 PM, Dave Messina <David.Messina at sbc.su.se>wrote:

> Nice, Chris!
>
> I've added it to the EUtils cookbook.
>
> Dave
>
>
>
> On Jun 10, 2010, at 2:06 AM, Chris Fields wrote:
>
> > It's much easier to work with the GI than the accession.  NCBI
> unfortunately just recently 'broke' their acc->gi stuff via efetch; you have
> to use rettype='seqid' and munge ASN.1 to get everything (though it is nice
> in a way for ID mapping).
> >
> > After the initial step of grabbing the GI for NG_011506, though, you can
> use elink to grab the SNP IDs, then use efetch to get the actual SNP files,
> or esummary for the summary info.
> >
> > #!/usr/bin/perl -w
> >
> > use Modern::Perl;
> > use Bio::DB::EUtilities;
> >
> > my $id = '224809339';
> >
> > my $eutil = Bio::DB::EUtilities->new(-eutil => 'elink',
> >                                     -id    => $id,
> >                                     -email  => 'setyourown at foo.bar',
> >                                     -verbose   => 1,
> >                                     -dbfrom => 'nuccore',
> >                                     -db  => 'snp',
> >                                     -cmd   => 'neighbor_history',
> > );
> >
> > my $hist = $eutil->next_History || die "No history data returned";
> >
> > $eutil->set_parameters(-eutil => 'efetch',
> >                       -history   => $hist,
> >                       -retmode => 'text',
> >                       # 'chr', 'flt', 'brief', 'rsr', 'docset'
> >                       -rettype => 'chr'
> > );
> >
> > $eutil->get_Response(-file => 'snps.txt');
> >
> > # or ...
> >
> > $eutil->set_parameters(-eutil => 'esummary',
> >                       -history   => $hist,
> > );
> >
> > $eutil->print_all;
> >
> > # chris
> >
> > On Jun 9, 2010, at 1:37 PM, Jessica Sun wrote:
> >
> >> Thanks Dave.
> >> the variation information is not present in the version of NG_011506 I
> found
> >> at Genbank.) -- Yes, then if you click on the right side customer view
> there
> >> is a check box Features added by NCBI :209 snps, if you check that it
> will
> >> add all the variations in the gbk fomat. I found this would be a neat
> >> feature if it can automatically load by bioperl with an option turn on.
> >>
> >>
> >>
> >> On Wed, Jun 9, 2010 at 1:51 PM, Dave Messina <David.Messina at sbc.su.se
> >wrote:
> >>
> >>> Hi Jessica,
> >>>
> >>> Please keep the BioPerl list on the Cc line so everyone can follow
> along.
> >>>
> >>>
> >>>> Follow your approach it did not seem to me you can have Variation tag
> >>> included which
> >>>> list the know dbSNP location, id and allele changes?
> >>>
> >>> Ah okay, I assumed the file you attached was obtained directly from
> Genbank
> >>> and that the variation info therein was already included. (It appears
> that's
> >>> not the case — the variation information is not present in the version
> of
> >>> NG_011506 I found at Genbank.)
> >>>
> >>> If you want to include your own custom information in a genbank file,
> >>> you'll have to pull it out of dbSNP (or wherever the variation info
> is).
> >>> There are a couple of scripts that might be able to help with that
> (search
> >>> for snp):
> >>>
> >>>      http://www.bioperl.org/wiki/Bioperl_scripts
> >>>
> >>>
> >>> You can then insert them into a RichSeq object as features and output
> in
> >>> genbank format. For that part, see the HOWTO:
> >>>
> >>>      http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> >>>
> >>>
> >>> Dave
> >>>
> >>>
> >>
> >>
> >> --
> >> Jessica Jingping Sun
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>


-- 
Jessica Jingping Sun