[Biopython-dev] Blast Parser error

Michiel De Hoon mdehoon at c2b2.columbia.edu
Wed Nov 23 13:10:20 EST 2005

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


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:

>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 :
>>#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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