[Biopython-dev] [BioPython] Biopython hackathon

[Peter]

Ann Loraine wrote:
> I hope you will consider the following two requests as possible
> hackathon activities:
> 
> (1) If it does not already do this, it would be nice if the blast
> "plain text" (non-XML) parser would report the length of the target
> ("hit") sequence as well as the query. If I recall correctly, the last
> time I used the plain text blast parser, I had to measure the length
> of the targets by opening up the fasta copy of the blastable database
> and reading the lengths one-by-one. My database wasn't very big, so it
> wasn't a hassle to do this, but I can foresee situations where this
> kludge would fail.

I'm not answering your question, but...

The "plain text" (non-XML) parser is currently falling behind the 
changes the NCBI seem to make each release - see bug 2090:

http://bugzilla.open-bio.org/show_bug.cgi?id=2090

We really want to encourage people to move over to the XML Blast parser 
instead.  Do you have a strong reason for preferring to parse the plain 
text output?

Peter