[BioPython] Problem with blastx output parsing =~

[Christof Winter]

Chris Fields wrote:
> 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.

I fully agree to that! I think the reason why people are still using the flat 
file format a lot is because they want to easily read it.

What these people are missing is probably an easy way to convert an XML Blast 
output to a plain text Blast report.

Would it then make sense include such a conversion script into BioPython? Maybe 
XSLT is the easiest option?

Cheers,
Christof