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<div class="moz-cite-prefix">Hi,<br>
<br>
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.<br>
It is more like a very convenient short cut.<br>
<br>
Michael<br>
<br>
On 11/12/12 08:20, Ada Lu wrote:<br>
</div>
<blockquote
cite="mid:001b01cdd778$5c35ced0$14a16c70$@genetics.ac.cn"
type="cite">
<pre wrap="">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?
</pre>
<br>
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<br>
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</pre>
</blockquote>
<br>
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