[Biopython-dev] Status of SearchIO

[Michiel de Hoon]

> 1. Bio.seq.search (in line with the namespace change)
> 2. Bio.seqsearch (top-level module, separate from Bio.seq. This used
>    to be Bio.SeqSearch, now adjusted for PEP8 compliance)
> 3. Bio.search (same reasoning + explanation like Bio.seqsearch).
> 4. Bio.SearchIO / Bio.searchio
> 5. Bio.psearch (p for pairwise)

> If it's down to a vote, I would vote to merge this branch as
> Bio.SearchIO, and perhaps lowercase it to Bio.searchio or
> biopy.searchio in the Py3 lowercase branch.
> 
> Rationale: We already follow BioPerl with SeqIO and AlignIO, and it
> seems to help users. It's also Google-friendly.

I would vote for Bio.seq.search.
I don't like Bio.SearchIO much because a) it doesn't tell you clearly what the module is about; and b) I think it it is a mistake to have Bio.SeqIO separate from Bio.Seq, and Bio.AlignIO separate from Bio.Align, because in both cases the two modules conceptually deal with the same thing. We don't have Bio.Cluster and Bio.ClusterIO, Bio.Entrez and Bio.EntrezIO, Bio.Motif and Bio.MotifIO; why should Bio.Seq and Bio.Align be different?

-Michiel.