[BioPython] Problem with blastx output parsing =~

[Chris Fields]

On Jun 4, 2007, at 12:05 PM, Peter wrote:

> ...
> It looks like you are using the plain text output from blast, so we
> would recommend you try the XML output instead.
>
> See section 3.4 of the tutorial:
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
>
> If you really want to use the plain text output, please file a bug
> (including Biopython version number) and then attach the plain text
> blast output which fails. But no promises - its an uphill battle to  
> keep
> the parser up to date with each version of Blast!
>
> Peter

Same with the bioperl parser; we routinely recommend parsing XML or  
tabular output as they are more stable.

Here is NCBI's official response (via Scott McGinnis) to problems  
with text BLAST output parsing:

http://bioperl.org/wiki/NCBI_Blast_email

chris