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

[Aurélie Bornot]

Thank you very much Alexander !!
I didn't dare to change the code in the Bio.Blast.NCBIWWW on my own because
I didn't have time to make tests...
So I simply automatiquely added the <p> in the Blast file... not very nice..
I know !
I will try your method instead !

Thanks !
Aurélie

--------------
Aurelie BORNOT
MNHN
Paris



----- Original Message ----- 
From: "Alexander A. Morgan" <amorgan at mitre.org>
To: <aurelie.bornot at free.fr>
Cc: <biopython at biopython.org>
Sent: Tuesday, August 02, 2005 10:07 PM
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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>
>
>
>