[BioPython] Changes in NCBI BLAST output format !!??

[Michiel De Hoon]

Do you happen to know if this change can break anything else in the Blast
parser? From running Biopython's tests for Blast, it seems that this change
is OK. On the other hand, I don't use Blast much myself, so I don't trust my
own judgement in this matter.
If making this change does not cause any new bugs, I'd be happy to include it
in CVS.

--Michiel.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-----Original Message-----
From: biopython-bounces at portal.open-bio.org on behalf of Alexander A. Morgan
Sent: Tue 8/2/2005 4:07 PM
To: aurelie.bornot at free.fr
Cc: biopython at biopython.org
Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??
 
Hello:
    I've just run into the same problem, and I haven't seen a suggested 
fix go by, so I apologize if this is redundant information, but it seems 
that the files I've been getting from NCBI have a <p> removed from the 
header between the "RID: " line and the "<p>Query" line, and it is just 
a blank line now.  If you edit Bio.Blast.NCBIWWW to not look for the 
"<p>", it seems to work okay.
 
class _Scanner:
....
   def _scan_header(self, uhandle, consumer):
....

    change:
        attempt_read_and_call(uhandle, consumer.noevent, start='<p>')
    to: 
        attempt_read_and_call(uhandle, consumer.noevent)





aurelie.bornot at free.fr wrote:

>Thank you very much Jessica !!!
>
>Unfortunately, I need a lot of thing in the BLAST reports.....
>It will be difficult to do the same thing as you did....
>
>I will try to do something in the code of parser of Python.
>But it will be difficult for me..
>so if you or someone has advices !!!
>
>Thanks a lot again for your answer Jessica !
>Aurélie
>
>
>--------------
>Aurelie BORNOT
>MNHN
>Paris
>
>
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>BioPython mailing list  -  BioPython at biopython.org
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>  
>


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