[Bioperl-l] get_Seq_by_id: CONTIG found

Chris Fields cjfields at uiuc.edu
Tue Jul 29 17:06:24 EDT 2008


It could also be a versioning issue.  Checking back through bioperl- 
live and the release branches, 'CONTIG found. GenBank  
get_Stream_by_acc about to run' is only in bioperl 1.4.  I suggest an  
update to 1.5.2 or bioperl-live.

chris

On Jul 29, 2008, at 2:44 PM, Kevin Brown wrote:

> Might be a proxy server issue as I notice the code snippet uses one.
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ocar  
>> campos
>> Sent: Tuesday, July 29, 2008 11:08 AM
>> To: melody; bioperl-l at portal.open-bio.org
>> Subject: Re: [Bioperl-l] get_Seq_by_id: CONTIG found
>>
>>
>> I got a very similar message when trying to access with a
>> Version Number, but saying that the sequence is not in the
>> db, and when I check via web, the sequence is there, and then
>> the script works.
>>
>> regards
>>
>> O'car
>>
>> ----------------------------------------
>>> From: xyuany at mail2.sysu.edu.cn
>>> To: bioperl-l at portal.open-bio.org
>>> Date: Tue, 29 Jul 2008 23:47:31 -0700
>>> Subject: [Bioperl-l]  get_Seq_by_id: CONTIG found
>>>
>>> I'm trying to download a bunch of sequences from GenBank
>> using the gi ,when
>>> I run the code,I got The message like this :
>>>
>>> -------------------- WARNING ---------------------
>>> MSG: CONTIG found. GenBank get_Stream_by_acc about to run.
>>> ---------------------------------------------------
>>> Warning: unable to close filehandle FETCH properly.
>>>
>>> What can I do if I want this code work.
>>> Thanks a lot,
>>> Melody xiong
>>>
>>>
>>> use Bio::DB::GenBank;
>>> my $db_obj = new Bio::DB::GenBank;
>>> $db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/');
>>>        my $seq_obj=$db_obj->get_Seq_by_gi("42537818");
>>>        my $seqio_obj=Bio::SeqIO->new(-file =>
>> ">temp2.txt", -format =>
>>> "fasta" );
>>>        $seqio_obj->write_seq($seq_obj);
>>>
>>>
>>>
>>>
>>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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