[Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1715

biopython-bugzilla at maubp.freeserve.co.uk changed:

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------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2005-02-16 16:53 -------
Created an attachment (id=194)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=194&action=view)
Edited version of NCBIStandalone.py based on CVS revision 1.57

This is a revised version of my previous "patch" to deal with iterating over
multiple RPS-BLAST outputs.

The implementation of the RPS Blast iteration is in my opinion ugly, but
functional.

It saves the database line (which is not repeated in RPS-BLAST output) and
re-inserts it before each Query= line (which marks the start of subsequent
results).

I have used this file extensively for parsing multi-query RPS Blast 2.0.10
output on both linux, Windows 2000, and to a lesser extent, Windows XP without
problem.

I doubt this code is worth of including in BioPython as is in the long term,
but maybe could be included BioPython 1.40 until something nicer is produced.

Alternatively, the previous version (without the Iterator cludge) is quite nice
code wise, and should provide full rpsblast support except for multiple input
queries.

Review?



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