[DAS] Need help about ProServer error

[Andy Jenkinson]

Hi,

The name, seq_region_start and seq_region_end variables are dynamic, they are supposed to be bound in the Perl module. It looks like your code doesn't match the example in the tutorial exactly. See the part that says "You can use ? placeholders to make the query generic for use with dynamic segment, start and end parameters. Click here to show/hide the code:"

Regards
Andy

On 12 Jun 2012, at 08:47, 陈岗 wrote:

> Hi All
> 
> I follow ProServer tutorial Part 3 (
> http://www.ebi.ac.uk/~aj/das_workshop_2012/proserver/tutorial3.html ), try
> to get the gene-exon data, but an error occurs. The SQl sentence is
> correct, I tried it on MySQL server.  what is the problem?
> 
> Bad data source exonsdb (error processing command: 'features')
> 
> The error was: 'Error running query: DBD::mysql::st execute failed:
> called with 3 bind variables when 0 are needed at
> blib/lib/Bio/Das/ProServer/SourceAdaptor/Transport/dbi.pm line 77.
> 
> Args were: Bio::Das::ProServer::SourceAdaptor::Transport::dbi=HASH(0xbc99e8)
> select sr.name AS chromosome,
>       g.stable_id AS g_id, g.seq_region_start AS g_start,
> g.seq_region_end AS g_end,
>       t.stable_id AS t_id, t.seq_region_start AS t_start,
> t.seq_region_end AS t_end,
>       e.stable_id AS e_id, e.seq_region_start AS e_start,
> e.seq_region_end AS e_end
> from   seq_region sr, coord_system c,gene g,transcript t,
> exon_transcript et, exon e
> where sr.seq_region_id = g.seq_region_id
> and g.gene_id = t.gene_id
> and t.transcript_id = et.transcript_id
> and sr.name = 'Y'
> and sr.coord_system_id = c.coord_system_id
> and c.name = 'chromosome'
> and c.version = 'GRCh37'
> and g.seq_region_end >= 1
> and g.seq_region_start <= 59373566
> and e.exon_id = et.exon_id
> Y 2800000 2900000
> at blib/lib/Bio/Das/ProServer/SourceAdaptor/EnsExon.pm line 38.'
> 
> Best Regards
> 
> -- 
> 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province,
> P.R.China
> Phone:（+86）512-82782588
> 
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