[Bioperl-l] need help urgently

Tue Sep 8 04:50:01 UTC 2009

Russell,

Any reason you're using "no warnings 'deprecated'" there?  The  
pseudohash warnings should no longer be showing up with EntrezGene  
stuff.  Or is it something else?

chris

On Sep 7, 2009, at 11:41 PM, Smithies, Russell wrote:

> 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
>>>>>
>>>>>
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