[Bioperl-l] default Bio::DB::SwissProt server broken?

Hamish McWilliam hamish.mcwilliam at bioinfo-user.org.uk
Wed Oct 27 11:34:09 EDT 2010


Hi Chris,

Although they handle the redirect, the other modules which use dbfetch
should probably have the URLs updated too:

Bio::DB::Biblio::biofetch
Bio::DB::EMBL
Bio::DB::RefSeq

Hamish

On 27 October 2010 15:51, Chris Fields <cjfields at illinois.edu> wrote:
> Hamish,
>
> Thanks, but I already caught that and fixed it in main trunk where appropriate yesterday (specifically, both Bio::DB::SwissProt and Bio::DB::BioFetch).
>
> chris
>
> On Oct 27, 2010, at 5:32 AM, Hamish McWilliam wrote:
>
>> Hi Chris,
>>
>> The dbfetch service at EBI has changed, see
>> http://www.ebi.ac.uk/Tools/webservices/about/news#st_october_2010. On
>> of the effects of this is the main endpoint used for dbfetch has
>> changed from http://www.ebi.ac.uk/cgi-bin/dbfetch to
>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch. With the old endpoints
>> being supported via a HTTP redirect. It looks like the
>> Bio::DB::SwissProt module does not support redirects and is thus
>> getting an empty document back from the service. Looks like the URL
>> used in the code needs to be updated.
>>
>> All the best,
>>
>> Hamish
>>
>> On 26 October 2010 23:02, Chris Fields <cjfields at illinois.edu> wrote:
>>> The default was changed recently in github to 'expasy'.  My guess is something changed on the EBI DBFetch end that isn't accepting certain identifiers anymore.
>>>
>>> chris
>>>
>>> On Oct 26, 2010, at 1:25 PM, Matthew Conte wrote:
>>>
>>>> Hello,
>>>>
>>>> I have a custom script for parsing out UniProt accessions from a GFF3 file
>>>> and fetching the description of the UniProt entry using Bio::DB::SwissProt
>>>> and *get_Seq_by_acc*.  This script has been working for months without any
>>>> problems until now.  The script and the format of the input files has not
>>>> changed at all.
>>>>
>>>> I now get an error like this:
>>>>
>>>> *------------- EXCEPTION: Bio::Root::Exception -------------*
>>>> *MSG: acc O95342 does not exist*
>>>> *STACK: Error::throw*
>>>> *STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368*
>>>> *STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
>>>> /Library/Perl/5.10.0/Bio/DB/WebDBSeqI.pm:195*
>>>> *STACK: /Users/Matt/scripts/get_uniprot_names.pl:35*
>>>> *-----------------------------------------------------------*
>>>>
>>>> The relevant portion of my original code looks something like this:
>>>>
>>>> *#!/usr/bin/perl*
>>>> *use strict;*
>>>> *use Bio::DB::SwissProt;*
>>>> *#parse out accession number*
>>>> *..*
>>>> *my $acc_num = "**O95342";*
>>>> *my $db_obj = Bio::DB::SwissProt->new;*
>>>> *my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);*
>>>> *
>>>> *
>>>> Looking at the documentation for Bio::DB::SwissProt, I noticed you can
>>>> specify -servertype and -hostlocation.  So I changed my code to look
>>>> something like this:
>>>>
>>>> *
>>>> #!/usr/bin/perl
>>>> use strict;
>>>> use Bio::DB::SwissProt;
>>>> #parse out accession number
>>>> ..
>>>> my $acc_num = "O95342";
>>>> my $db_obj = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>>>                                                           '-hostlocation'
>>>> => 'us');
>>>> my $seq_obj = $db_obj->get_Seq_by_acc($acc_num);
>>>> *
>>>>
>>>> This fixes my problem and my script works again.
>>>>
>>>> The default *hostlocation *is http://www.ebi.ac.uk/cgi-bin/dbfetch and the
>>>> 'us' *hostlocation *is http://us.expasy.org/cgi-bin/sprot-retrieve-list.pl.
>>>>  Both of these urls work in a browser, though the default throws the error
>>>> in my script. Interestingly, the 'us' url has a notice that says
>>>> "*Notice:* This
>>>> page will be replaced with www.uniprot.org. Please send us your
>>>> feedback<http://www.uniprot.org/contact>
>>>> !", so hopefully it doesn't break soon as well.  Perhaps the default ebi url
>>>> was recently changed in some way?  Anyway, I figured I'd post here in case
>>>> anyone else ran into this problem.
>>>>
>>>> cheers,
>>>> Matt
>>>> _______________________________________________
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>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
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>>
>>
>>
>> --
>> ----
>> "Saying the internet has changed dramatically over the last five years
>> is cliché – the internet is always changing dramatically" - Craig
>> Labovitz, Arbor Networks.
>>
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>



-- 
----
"Saying the internet has changed dramatically over the last five years
is cliché – the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.



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