[Bioperl-l] SeqHound

Chris Fields cjfields at uiuc.edu
Tue Feb 5 17:59:48 EST 2008


On Feb 5, 2008, at 4:31 PM, Susan J. Miller wrote:

> Chris Fields wrote:
>> The URL has changed.  I'll fix this in bioperl-live.
>> You can fix this in your script directly for now (though I hate  
>> globals):
>> use Bio::DB::SeqHound;
>> $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' 
>> ;
>
> Thanks Chris, that helps a little bit, but I'm still not having much  
> luck with the SeqHound DB.  The CPAN SeqHound.pm documentation for  
> the get_Stream_by_Query method says:
> ...

No problem.  It was an easy fix.

...
> I get the error:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Id list has been truncated even after maxids requested
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/ 
> 5.8.8/Bio/DB/Query/WebQuery.pm:236
> STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/ 
> Bio/DB/Query/WebQuery.pm:200
> STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/SeqHound.pm:314
> STACK: SeqHoundQuery.pl:21
>
> There are only 5013 sequences that match this query so it seems odd  
> that the Id list is too long...or am I using SeqHound improperly?
>
> (My reason for trying SeqHound is that I want to set up a monthly  
> cron job to download nucest fasta sequences for drosphila  
> melanogaster, and I've tried NCBI E-Utilities and the script  
> generated by the NCBI ebot and in both cases some of the 570828  
> records get dropped, even after running repeated attempts.)
>
>
> Thanks,
> -susan


The URL is likely way too long (a common problem when using a GET as  
opposed to a POST with LWP).  NCBI's efetch has the same problem,  
which is why using epost is a good idea (except it only takes GI's!).   
You will have to loop through the IDs in bunches of 250-500 max to get  
what you want.

Don't know if there is a way to post to SeqHound but it might be worth  
investigating at some point.  I also see they have a SOAP interface up.

chris



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