[Biopython-dev] [Biopython] Parsing large blast files

[Michiel de Hoon]

--- On Tue, 4/28/09, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> I do like the idea of moving/importing the qblast function
> directly under Bio.Blast, and perhaps removing Bio.Blast.NCBIXML
> later on.

Well Bio.Blast.NCBIXML would still be there (containing the code for the XML parser), but users would access it through Bio.Blast.parse/read.
 
> For read/parse functions, we should probably call the
> format "blastxml" to match BioPerl.

We could have both "xml" and "blastxml" for Blast XML output, "text" and "blasttext" for Blast text output, and "table" and "blasttable" for Blast table (-m 8 and 9) output.

> Would you continue to support the plain text output here?

Yes. I'm more thinking about code reorganization than removing/adding functionality.

> Rather than continuing to encourage the use of blastall,
> blastpgp and rpsblast I would rather bring Bio.Blast.Applications
> up to date, and then declare them obsolete.

How would users typically use Bio.Blast.Applications?

--Michiel.