[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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