[Bioperl-pipeline] Re: Converter & filter

[Elia Stupka]

> 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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