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</o:shapelayout></xml><![endif]--></head><body lang=ZH-CN link=blue vlink=purple style='text-justify-trim:punctuation'><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Hi,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>When I do genebuild, I come across the warning,<o:p></o:p></span></p><p class=MsoNormal><b><span lang=EN-US>-------------------- WARNING ----------------------<o:p></o:p></span></b></p><p class=MsoNormal><b><span lang=EN-US>MSG: You should explicitely attach an analysis object to the Transcript. Will fall back to Gene analysis, but this behaviour is deprecated.<o:p></o:p></span></b></p><p class=MsoNormal><b><span lang=EN-US>FILE: EnsEMBL/DBSQL/TranscriptAdaptor.pm LINE: 798<o:p></o:p></span></b></p><p class=MsoNormal><b><span lang=EN-US>CALLED BY: EnsEMBL/DBSQL/GeneAdaptor.pm LINE: 1278<o:p></o:p></span></b></p><p class=MsoNormal><b><span lang=EN-US>Date (localtime) = Fri Dec 7 19:34:45 2012<o:p></o:p></span></b></p><p class=MsoNormal><b><span lang=EN-US>Ensembl API version = 69<o:p></o:p></span></b></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>These are Some script in TranscriptAdaptor.pm<o:p></o:p></span></p><p class=MsoNormal style='text-indent:5.25pt'><span lang=EN-US>784 # store analysis<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 785 my $analysis = $transcript->analysis();<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 786 my $new_analysis_id;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 787<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 788 if ($analysis) {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 789 if ( $analysis->is_stored($db) ) {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 790 $new_analysis_id = $analysis->dbID;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 791 } else {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 792 $new_analysis_id = $db->get_AnalysisAdaptor->store($analysis);<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 793 }<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 794 } elsif ($analysis_id) {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 795 # Fall back to analysis passed in (usually from gene) if analysis<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 796 # wasn't set explicitely for the transcript. This is deprectated<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 797 # though.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 798 warning( "You should explicitely attach "<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 799 . "an analysis object to the Transcript. "<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 800 . "Will fall back to Gene analysis, "<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 801 . "but this behaviour is deprecated." );<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 802 $new_analysis_id = $analysis_id;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 803 } else {<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 804 throw("Need an analysis_id to store the Transcript.");<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US> 805 }<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>It may treat transcript as gene, and it will lead to too many genes. Can somebody help me about it?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></body></html>