[Bioperl-pipeline] Genscan pipeline with EnsEMBL 9

[Xiao Juguang]

Hi guys,

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
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2) 2 converters have been developed, since one is an attachment of the other, as you know.

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.
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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.