Re: [GMOD-devel] getting JBrowse to run off a Chado database where feature.name field is not used

[Giles V. <gv...@sa...>]

Thanks for the quick reply, Scott! I am using the version available on  
cpan, but I am happy to take it to the bleeding edge, though! :)

Using the view does get me a bit further, thanks, but now it stops at

DBD::Pg::st execute failed: ERROR:  syntax error at end of input
LINE 3:      where feature_id =
                                  ^ at /usr/local/share/perl/5.10.0/ 
Bio/DB/Das/Chado/Segment.pm line 1641.

The line that's failing is in Segment->dna() :

	$sth->execute or $self->throw("seq query failed");

which means that for some reason $self->{srcfeature_id} is not set in  
that instance.

Best,
Giles


On 17 Sep 2009, at 14:44, Scott Cain wrote:

> Hi Giles,
>
> I have a few suggestions/questions for you:
>
> What version of Bio::DB::Das::Chado are you using?
>
> Do you have a view called all_feature_names?  If so, it should have
> found LmjF10.0010 since it searches over feature.name,
> feature.uniquename and synonym.name.  If you don't have it, you can
> get the sql for it from svn:
>
>  http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/modules/sequence/sequence_views.sql?revision=21980
>
> Sorry about the lower casing, though there should be functional
> indexes on lower(name) and the like in the database to make the
> comparisons go faster.
>
> Scott
>
>
> On Thu, Sep 17, 2009 at 9:27 AM, Giles Velarde <gv...@sa...>  
> wrote:
>> Hi there,
>>
>> I have been trying to set up JBrowse to run off Chado using the
>> Bio::DB::Das::Chado config. Although I am calling a JBrowse script,
>> the problem appears to be in the Das::Chado library.
>>
>> If I try to run :
>>
>>        $ ./bin/prepare-refseqs.pl --conf conf-chado.json --refs  
>> LmjF10.0010
>>
>> where "LmjF10.0010" corresponds to the Chado uniquename of a Gene
>> (with logging on), I get :
>>
>>
>> na:LmjF10.0010, id:, Bio::DB::Das::Chado=HASH(0x9914f80)
>> base_start = , stop =
>> quoted name:'lmjf10.0010'
>>  and rank = 0  and srcf.is_obsolete = false  at /usr/local/share/ 
>> perl/
>> 5.10.0/Bio/DB/Das/Chado/Segment.pm line 174.
>> _search_by_name args:Bio::DB::Das::Chado=HASH(0x9914f80)
>> 'lmjf10.0010'   at /usr/local/share/perl/5.10.0/Bio/DB/Das/Chado/
>> Segment.pm line 488.
>> looking for a synonym to 'lmjf10.0010' at /usr/local/share/perl/ 
>> 5.10.0/
>> Bio/DB/Das/Chado/Segment.pm line 524.
>> looking in dbxref for 'lmjf10.0010' at /usr/local/share/perl/5.10.0/
>> Bio/DB/Das/Chado/Segment.pm line 547.
>> no segment found at /usr/local/share/perl/5.10.0/Bio/DB/Das/Chado/
>> Segment.pm line 386.
>> Can't call method "name" on an undefined value at ./bin/prepare-
>> refseqs.pl line 72.
>>
>>
>> The "LmjF10.0010" gets lowercased to "lmjf10.0010" during the quoting
>> process, which slows the query down by having to use lower(). But
>> after looking into it I see that that's not the problem, the  
>> resulting
>> query is
>>
>>        select name,feature_id,seqlen from feature where lower(name) =
>> 'lmjf10.0010'  and is_obsolete = false  ;
>>
>> for the query work on our Chado database we would have to do :
>>
>>        select uniquename,feature_id,seqlen from feature where
>> lower(uniquename) = 'lmjf10.0010'  and is_obsolete = false  ;
>>
>> because, though we sometimes do use the name field, it's often not
>> used. We always use the uniquename, of course, because it's  
>> unique! :-)
>>
>> Best,
>> Giles
>>
>>
>>
>>
>>
>> --
>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>  Limited, a charity registered in England with number 1021457 and a
>>  company registered in England with number 2742969, whose registered
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>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.