[Bioperl-pipeline] Re: Converter & filter
Elia Stupka
elia@fugu-sg.org
Mon, 26 Aug 2002 10:58:32 +0800 (SGT)
> 1. Maybe we can have a method get_filtered_features() as the input method to
> these module
> which calls get _all_similarity_features_above_score.
Sounds good, make sure it takes as argument some kind of parameter so that
we can apply different filters if we want to.
> 2. We have to store these protein id and contig,start,end pair somewhere
> right?? prior to be fetched by the genewise input
> method???? where do we store them??
No they are in memory and are stored directly as input for
genewise. I just realised the simplest way to do that is to use as Output
IOHandler the bioperl-pipeline InputAdaptor, and simply use a store
method there! :)
> 3. why do we need the "contig,start,end" information?? I thought the
> repeat_masked_seq and the protein should suffice for the genewise??
Yes, the repeatmasked_seq but not of the whole scaffold, otherwise
genewise will run forever, only, the regions around the filtered hits.
Elia
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