[Biopython-dev] Blast Parser error

[Michiel De Hoon]

Can you use the XML parser in NCBIXML instead?
See the updated tutorial on the biopython website on how to use it.

--Michiel.

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



-----Original Message-----
From: biopython-dev-bounces at portal.open-bio.org on behalf of Matteo
Sent: Tue 11/22/2005 4:53 AM
To: Frederic Sohm
Cc: biopython-dev at biopython.org
Subject: Re: [Biopython-dev] Blast Parser error
 
Frederic Sohm ha scritto:

>Hi, 
>
>Just guessing.
>Did you check that blast_results is correct ?
>What did you get in error_info ?
>  
>
If I put a "print error_info" I get something like:
<open file 'C:\PATH\TO\PROGRAM\blastall.exe -p blastn -d 
C:\PATH\TO\PROGRAM\refsets.fasta -i C:\PATH\TO\PROGRAM\query.fasta', 
mode 'r' at 0x00AF6AD0>

>If everything is normal there, then the end of line is different in windows 
>('\r\n') and linux ('\n'), it might just be that.
>So try :
>
>...
>  
>
>>save_file.write(blast_results)
>>save_file.close()
>>#blast_out = open('my_blast.out', 'r')
>>    
>>
>blast_out = open('my_blast.out', 'rU')
>
>  
>
>>blastparser = NCBIStandalone.BlastParser()
>>alignrecord = blastparser.parse(blast_out)
>>[...]
>>    
>>
>
>  
>
At the end of the program the output "my_blast.out" is blank! I tried to 
launching blastall from the command line and THEN parsing the output 
with biopython, in this way it works! Maybe NCBIStandalone has a 
problem...I have downloaded the CVS versione but there is no change...
And remember that the SAME code works on linux...I also tried to 
download the versione that I have on my Ubuntu Linux (2.2.10) but there 
is no change...
Thank you for helping me,

Matteo De Felice
University of Rome "Roma Tre"

 
 
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