[Biopython-dev] Blast table parser

Iddo Friedberg idoerg at burnham.org
Wed Jan 29 06:24:03 EST 2003

Jeffrey Chang wrote:
>>The blast table parser is pretty much ready, should it go in 
>>NCBIStandalone.py, or should I set up a different file for it under 
> What does it do?  Does it parse things into a Bio/Blast/Record
> structure, or something different?  How much code is it?

It parses a BLAST output table (formatted through "blastpgp -m 9"). 
Since this table does not contain a sequence alignments, and it does 
contain other stuff, I don't think that the Bio/Blast/Record object is 
suitable, so I created two new classes, BlastTableRec, which can have 0 
or more BlastTableEntry(s) in it. Actually, I already commited it 
(sorry...) so you can have a look. Let me know how you would like me to 
modify it. If you think I can do this with the Bio/Blast/Record let me 
know, I will make an effort.

There isn't a lot of code, about 100 lines. The file is ParseBlastTable.py

Tangentially related: do we have a way of _easily_ taking an MSA from 
PSI-BLAST and putting in the multiple sequence alignment class?


> It should go into NCBIStandalone, unless there's a lot of code, or
> it's structurally different from the rest of the code in there.
> Jeff

Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

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