[Bioperl-pipeline] Genscan pipeline with EnsEMBL 9
Elia Stupka
elia@fugu-sg.org
Tue, 7 Jan 2003 14:23:00 +0800
> 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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