[Bioperl-pipeline] Genscan pipeline with EnsEMBL 9

[Elia Stupka]

> 1) I just finished the genscan pipeline with data from and to EnsEMBL 
> 9 db. The design file is xml/templates/juguang_genscan_annotation.xml
> -----
> 2) 2 converters have been developed, since one is an attachment of the 
> other, as you know.
>


Great! Did you check that the genscan peptides that are stored in 
Ensembl translate correctly, i.e. give the same translation that is 
given originally by Genscan?

Elia


> Bio::Pipeline::Converter::PredictionGeneToEnsEMBLConverter converts 
> objects of Bio::Tools::Prediction::Gene to 
> Bio::EnsEMBL::PredictionTranscript.
>
> Bio::Pipeline::Converter::PredictionExonToEnsEMBLConverter converts 
> objects of Bio::Tools::Prediction::Exon to Bio::EnsEMBL::Exon.
> ----
> 3) I make a slight change on Bio::Pipeline::Runnable::Genscan.
> 3.1) "$analysis->parameters" is replaced with 
> "$analysis->analysis_parameters"
> 3.2) This is the only case I find that the analysis's parameter is not 
> in "-tag value" pairs, so I avoid it from inovking RunnableI's 
> parse_params.
>
>
> Juguang.
>
>
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