Biopython xml parser for psiblast outputs

Question

[nvijay.1991]

HI all,

I am wondering that, is there any way to parse the PSIBLAST output at each iteration and check for the hits conservation and if condition get satisfied then only perform next iteration.

For example:

iteration 1 : hit1; hit2; hit3; hit4

case1: hits from iteration 1 are conserved - proceed further to iteration 3

iteration 2: hit1; hit2; hit3; hit4; hit5 (check for the conserved hits from iteration 1)

iteration 3: executed

case 2: hits from iteration 1 are not conserved/lost in iteration 2 - stop proceeding further to iteration 3

iteration 2: hit1; hit2; hit3; hit5(hit4 is missing;hence stop iterations to next level)

iteration 3: not executed

This was just a basic example I have shown, these can proceed further to next iterations till the previous iterations hits are conserved from top to bottom.

Thanks in advance,
Vijay N

[Peter]

The (version one) BLAST XML output has <Iteration> tags originally designed for PSI-BLAST, but later used/abused to support multiple queries in traditional BLAST output. Unfortunately for your use, the Biopython BLAST XML parser focuses on this second case. I have not yet investigated how BLAST XML 2 works for PSI-BLAST.

However, the is an old PSI-BLAST plain text parser still in Biopython which might be worth a look?

[nvijay.1991]

Thnak you Peter..

[Xylanaser]

Hey nvijay. Do u used the old PSIBLAST parser? I have a problem with parsing some data ;/ from PSIBLAST.... Can u give me advice?