[Bioperl-pipeline] How annotation biopipe store the analysis into ensembl, automatically.

[Juguang Xiao, TLL]

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