[Bioperl-l] need help urgently

[Neeti Somaiya]

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_database

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::GenBank_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
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>
>