[Bioperl-pipeline]
How annotation biopipe store the analysis into ensembl,
automatically.
Juguang Xiao, TLL
juguang at tll.org.sg
Thu Mar 20 12:15:06 EST 2003
HI all,
First of all, please cvs update your ensembl copy. When annotation is
referred here, I mean to store such annotation into ensembl database.
The new transformer system considers the conversion and storage of
analysis, if you want to save the result into ensembl db.
As you found, both db schema and perl object between biopipe Analysis
and ensembl-pipeline Analysis are very similar. That makes analysis
conversion work a lot easy. (maybe that is bad on less consideration on
other project, such as bioperl-db ??)
When you create your biopipe xml, you should fill in the information of
analysis as much as necessary, which is promised to be stored in the
ensembl table later, shown below
<analysis id="2">
<logic_name>RepeatMask</logic_name>
<db>repbase</db>
<db_version>001212</db_version>
<db_file></db_file> <!-- No pushing, if you do not know, or analysis
does not require that -->
<program></program>
<program_version> </program_version>
<program_file> </program_file>
<parameters> </parameters>
<module> </module>
<module_version> </module_version>
<gff_source></gff_source>
<gff_feature></gff_feature>
</analysis>
So when you try to convert the bioperl seqfeaure or a sort of objects
into ensembl ones. As you know, you have to offer the ensembl contig
and analysis to the converter, so the Converter::new is the place for
you to specify it.
my $converter = Bio::EnsEMBL::Utils::Converter(
-in => 'Bio::SeqFeature::Generic',
-out => 'Bio::EnsEMBL::SimpleFeature',
-analysis => $ens_analysis, # or $biopipe_analysis !!
-contig => $ens_rawContig
);
Any questions?
Juguang
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