[ensembl-dev] You should explicitely attach an analysis object to the Transcript

Michael Paulini mh6 at sanger.ac.uk
Tue Dec 11 09:36:50 GMT 2012


Hi,

no it only will use the same analysis object and connect it to the genes
and transcripts. Else you have to define a specific analysis every time.
It is more like a very convenient short cut.

Michael

On 11/12/12 08:20, Ada Lu wrote:
> Hi,
>
> When I do genebuild, I come across the warning,
>
> -------------------- WARNING ----------------------
>
> MSG: You should explicitely attach an analysis object to the Transcript.
> Will fall back to Gene analysis, but this behaviour is deprecated.
>
> FILE: EnsEMBL/DBSQL/TranscriptAdaptor.pm LINE: 798
>
> CALLED BY: EnsEMBL/DBSQL/GeneAdaptor.pm  LINE: 1278
>
> Date (localtime)    = Fri Dec  7 19:34:45 2012
>
> Ensembl API version = 69
>
>  
>
> These are Some script in TranscriptAdaptor.pm
>
> 784   # store analysis
>
> 785   my $analysis = $transcript->analysis();
>
> 786   my $new_analysis_id;
>
> 787
>
> 788   if ($analysis) {
>
> 789     if ( $analysis->is_stored($db) ) {
>
> 790       $new_analysis_id = $analysis->dbID;
>
> 791     } else {
>
> 792       $new_analysis_id = $db->get_AnalysisAdaptor->store($analysis);
>
> 793     }
>
> 794   } elsif ($analysis_id) {
>
> 795     # Fall back to analysis passed in (usually from gene) if analysis
>
> 796     # wasn't set explicitely for the transcript. This is deprectated
>
> 797     # though.
>
> 798     warning(   "You should explicitely attach "
>
> 799              . "an analysis object to the Transcript. "
>
> 800              . "Will fall back to Gene analysis, "
>
> 801              . "but this behaviour is deprecated." );
>
> 802     $new_analysis_id = $analysis_id;
>
> 803   } else {
>
> 804     throw("Need an analysis_id to store the Transcript.");
>
> 805   }
>
>  
>
> It may treat transcript as gene, and it will lead to too many genes. Can
> somebody help me about it?
>
>  
>
>
>
>
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