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

[Ada Lu]

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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