[Biopython-dev] SearchIO, was: PEP8 lower case module names?

[Wibowo Arindrarto]

Hi everyone,

>> However, I also added code to additionally test
>> Bio.SearchIO.index_db(...).get_raw(...) as well as your
>> original testing of Bio.SearchIO.index(...).get_raw(...)
>> alone. These should return the exact same string, and
>> that is now working nicely for BLAST XML (and BGZF
>> from limited testing), but not on all the formats.
>>
>> Could you look at the difference in get_raw and the
>> record length found during indexing for: blast-tab
>> (with comments), hmmscan3-domtab, hmmer3-tab,
>> and hmmer3-text?
>>
>> i.e. Anything where test_SearchIO_index.py is now
>> printing a WARNING line when run.
>
> Sure :). Based on a quick initial look, it seems that these are due to
> filler texts (e.g. the BLAST
> tab format ending with lines like "# BLAST processed 3 queries").
> These texts won't affect the calculation results and the values of our
> objects, but does add additional text length.

I've looked into this and submitted a pull request to fix the issues
here: https://github.com/biopython/biopython/pull/111. The details on
the errors are also there.

regards,
Bow