[Biopython-dev] Status of SearchIO

[Peter Cock]

On Fri, Oct 26, 2012 at 4:19 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> Bio.Blast does contain some features beyond parsing the output of BLAST...
>

Also wrappers to call the tools, and the online search.
Easy enough.

>> Reaching a unanimous decision on name preference seems difficult :/.
>> We now have:
>>
>> 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)
>>
>> Any other suggestions? Should we put it to a vote?
>>
>> regards,
>> Bowo
>>
>
> 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 like Bio.SearchIO for those reasons too. Perhaps that is the
most popular name?

Peter