[Bioperl-l] need help urgently

[Smithies, Russell]

That bit of code gave you the accession, start and end for the sequence so you just needed to download it.
Bio::DB::Eutilities can do that for you.

Did you take a look at http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences



--Russell

==================
#!perl -w

use strict;
use Bio::DB::EntrezGene;
use Bio::DB::EUtilities;

no warnings 'deprecated';
 
my $id = shift or die "Id?\n"; # use a Gene id
 
my $db = new Bio::DB::EntrezGene;
#$db->verbose(1);
my $seq = $db->get_Seq_by_id($id);
 
my $ac = $seq->annotation;
 
for my $ann ($ac->get_Annotations('dblink')) {
	if ($ann->database eq "Evidence Viewer") {
                # get the sequence identifier, the start, and the stop
		my ($acc,$from,$to) = $ann->url =~
		  /contig=([^&]+).+from=(\d+)&to=(\d+)/;
		print "$acc\t$from\t$to\n";

		# retrieve the sequence
		my $fetcher = Bio::DB::EUtilities->new(-eutil => 'efetch',
					   -db    => 'nucleotide',
					   -rettype => 'fasta');
            $fetcher->set_parameters(-id => $acc,
			     			-seq_start => $from,
			     			-seq_stop  => $to,
			     			-strand    => 1);
            my $seq = $fetcher->get_Response->content;
            print $seq;

	}
}

======================

> -----Original Message-----
> From: Neeti Somaiya [mailto:neetisomaiya at gmail.com]
> Sent: Tuesday, 8 September 2009 4:28 p.m.
> To: Smithies, Russell
> Cc: Emanuele Osimo; bioperl-l
> Subject: Re: [Bioperl-l] need help urgently
> 
> I actually want the nucleotide sequence of the gene. I thought the
> Bio::DB::EntrezGene would give me a seq_obj for an entrez gene id and
> then the seq method on that $seq_obj->seq() will give me the actual
> genomic nucleotide sequence of the gene. But this doesnt happen. I am
> able to print gene symbol using $seq_obj->display_id and able to do
> other things, but I wanted the gene nucleotide sequence.
> 
> -Neeti
> Even my blood says, B positive
> 
> 
> 
> On Tue, Sep 8, 2009 at 1:56 AM, Smithies,
> Russell<Russell.Smithies at agresearch.co.nz> wrote:
> > This example code from the wiki _definitely_ works:
> >
> http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_Bio::DB::Entrez
> Gene_to_get_genomic_coordinates
> > =========================================
> >
> > use strict;
> > use Bio::DB::EntrezGene;
> >
> > my $id = shift or die "Id?\n"; # use a Gene id
> >
> > my $db = new Bio::DB::EntrezGene;
> > $db->verbose(1); ###
> >
> > my $seq = $db->get_Seq_by_id($id);
> >
> > my $ac = $seq->annotation;
> >
> > for my $ann ($ac->get_Annotations('dblink')) {
> >        if ($ann->database eq "Evidence Viewer") {
> >                # get the sequence identifier, the start, and the stop
> >                my ($contig,$from,$to) = $ann->url =~
> >                  /contig=([^&]+).+from=(\d+)&to=(\d+)/;
> >                print "$contig\t$from\t$to\n";
> >        }
> > }
> >
> > ======================================
> >
> > So if it doesn't work for you, there are a few things you need to check:
> > * what version of BioPerl are you using?
> > * are you behind a firewall?
> > * are you using a proxy?
> > * do you need to submit username/password for either of the 2 above
> > * turn on 'verbose' messages, it may help you debug
> >
> >
> > If you're still having problems, get back to me and I'll see if I can help.
> >
> > --Russell
> >
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >> bounces at lists.open-bio.org] On Behalf Of Neeti Somaiya
> >> Sent: Monday, 7 September 2009 10:04 p.m.
> >> To: Emanuele Osimo; bioperl-l
> >> Subject: Re: [Bioperl-l] need help urgently
> >>
> >> I tried using EntrezGene instead of GenBank, as is given in the link
> >> that you sent :
> >>
> >>
> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_datab
> >> ase
> >>
> >> http://doc.bioperl.org/releases/bioperl-current/bioperl-
> >> live/Bio/DB/EntrezGene.html
> >>
> >> use Bio::DB::EntrezGene;
> >>
> >>     my $db = Bio::DB::EntrezGene->new;
> >>
> >>     my $seq = $db->get_Seq_by_id(2); # Gene id
> >>
> >>     # or ...
> >>
> >>     my $seqio = $db->get_Stream_by_id([2, 4693, 3064]); # Gene ids
> >>     while ( my $seq = $seqio->next_seq ) {
> >>           print "id is ", $seq->display_id, "\n";
> >>     }
> >>
> >> This doesnt seem to work.
> >>
> >>
> >> -Neeti
> >> Even my blood says, B positive
> >>
> >>
> >>
> >> On Fri, Sep 4, 2009 at 1:09 PM, Emanuele Osimo<e.osimo at gmail.com> wrote:
> >> > Hello,
> >> > have you tried this?
> >> >
> >>
> http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_Bio::DB::GenBan
> >> k_when_you_have_genomic_coordinates
> >> >
> >> > Emanuele
> >> >
> >> > On Fri, Sep 4, 2009 at 08:49, Neeti Somaiya <neetisomaiya at gmail.com>
> wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> I have an input list of gene names (can get gene ids from a local db
> >> >> if required).
> >> >> I need to fetch sequences of these genes. Can someone please guide me
> >> >> as to how this can be done using perl/bioperl?
> >> >>
> >> >> Any help will be deeply appreciated.
> >> >>
> >> >> Thanks.
> >> >>
> >> >> -Neeti
> >> >> Even my blood says, B positive
> >> >> _______________________________________________
> >> >> Bioperl-l mailing list
> >> >> Bioperl-l at lists.open-bio.org
> >> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >
> >> >
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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