[Bioperl-l] problem with batch access to GenBank

[Anne-Marie Ternes]

Hi Brian,

thanks a lot for your help. As a matter of fact, I came to have a
serious look at what was effectively contained in the array I passed to
"get_Stream_by_acc".
What happened was that my dear Windows had put "^M"s into the file
containing the accession numbers. Those were then read into the array,
and passed to NCBI together with the offending "^M"s, which of course
can not get any results.
Not that I didn't look for that in my file, but unfortunately none of my
Linux editors, except good ol' Emacs, showed the "^M"s at all.

So, in conclusion, a dumb mistake ;-)

Anne-Marie

On Tue, 3 Jun 2003 13:44:24 -0400
"Brian Osborne" <brian_osborne at cognia.com> wrote:

> Anne-Marie,
> 
> > So I wonder if there might be some obscure difference in implementation
> > between "get_Seq_by_acc" and "get_Stream_by_acc".
> 
> Without seeing your code it's hard to know for certain but you may be doing
> something odd with your stream. From the bptutorial:
> 
>   $gb = new Bio::DB::GenBank();
>   # this returns a Seq object :
>   $seq1 = $gb->get_Seq_by_id('MUSIGHBA1');
>   # this returns a Seq object :
>   $seq2 = $gb->get_Seq_by_acc('AF303112');
>   # this returns a SeqIO object :
>   $seqio = $gb->get_Stream_by_id(["J00522","AF303112","2981014"]);
> 
> If this is not helpful then you might consider showing us the offending
> code.
> 
> Brian O.
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Anne-Marie Ternes
> Sent: Tuesday, June 03, 2003 1:11 PM
> To: bioperl-l at bioperl.org
> Cc: Anne-Marie Ternes
> Subject: [Bioperl-l] problem with batch access to GenBank
> 
> Hello,
> 
> I've got a problem for submitting a batch of gene accession numbers to
> GenBank.
> 
> I simply use the Bio::DB::GenBank package for creating a new GenBank
> instance, and then use the "get_Stream_by_acc" method, passing it an
> array of accession numbers as parameter.
> Unfortunately, I don't get any results from this query. It seems to run
> OK, as I get no connection error messages, it just ignores my subsequent
> "while" loop looking for the next sequence in the result set.
> 
> Although I'm a PERL newbie, I'm not a network dummy, so I'm totally sure
> I'm not behind a proxy, nor behind a firewall. I have unset any
> environment variables related to proxies.
> I'm also sure that the array effectively contains accession numbers in
> correct formats.
> 
> Another bit of code, that resembles the problematic one for one single
> difference: it uses "get_Seq_by_acc" with a single accession number as
> parameter, runs perfectly:
> information regarding enzyme numbers are correctly retrieved, and later
> passed to a KEGG query.
> 
> So I wonder if there might be some obscure difference in implementation
> between "get_Seq_by_acc" and "get_Stream_by_acc".
> 
> By the way, I have also checked using "netstat" that connections to NCBI
> get properly established, which is the case.
> 
> If anyone has an idea what might be going on, I can't say how glad I'd
> be! I'm in fact a bioinformatics MSc student, and ironically, my code
> runs perfectly on my pal's computers, but not on mine ;-)
> 
> Thanks a lot in advance,
> 
> Anne-Marie Ternes
> amternes at pt dot lu
> 
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-----------------------------------------------------------------------------------------------------------
Anne-Marie Ternes

Blessed is he who has learned to laugh at himself for he shall never cease to be entertained.
John Powell.