[Bioperl-l] RefSeq

[Jessica Sun]

Great. Thanks .

On Sat, Mar 13, 2010 at 3:29 PM, Siddhartha Basu <sidd.basu at gmail.com>wrote:

> The following code works with 1.6.1 of bioperl. It uses eutils and the
> workflow efetch -> elink -> esummary.
>
> #!/usr/bin/perl -w
>
> use strict;
> use Bio::DB::EUtilities;
>
> my $id = $ARGV[0] || 'NM_001618';
>
> my $eutils = Bio::DB::EUtilities->new(
>    -eutil      => 'esearch',
>    -db         => 'nucleotide',
>    -term       => $id,
>    -usehistory => 'y'
> );
>
> my $hist = $eutils->next_History || die "no history\n";
>
> $eutils->reset_parameters(
>    -eutil          => 'elink',
>    -db             => 'gene',
>    -dbfrom         => 'nuccore',
>    -history        => $hist
> );
>
> my ($gene_id) = $eutils->next_LinkSet->get_ids;
>
> $eutils->reset_parameters(
>    -eutil => 'esummary',
>    -db    => 'gene',
>    -id    => $gene_id,
> );
>
> my ($item) = $eutils->next_DocSum->get_Items_by_name('GenomicInfoType');
> print $item->get_contents_by_name('ChrAccVer'),  "\n";
>
> -siddhartha
>
> On Fri, 12 Mar 2010, Jessica Sun wrote:
>
> > I have a question: I have a refseq with NM_ number(mRNA), how can I get
> > the genomic sequences(NT_number) with Bioperl, if it can be done?
> >
> > Thanks
> >
> >
> > --
> > Jessica Jingping Sun
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
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>



-- 
Jessica Jingping Sun