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BLAST Database Error for Biopython

I try to run blastx locally with the "nr" database using the Biopython NcbiblastxCommandline tool, but I always get the following error regarding the protein database search path:

>>> from Bio.Blast.Applications import NcbiblastxCommandline
>>> nr = "/Users/Priya/Documents/Python/ncbi-blast-2.2.26+/bin/nr.pal"
>>> infile = "/Users/Priya/Documents/Python/Tutorials/opuntia.txt"
>>> blastx = "/Users/Priya/Documents/Python/ncbi-blast-2.2.26+/bin/blastx"
>>> outfile = "/Users/Priya/Documents/Python/Tutorials/opuntia_python_local.xml"
>>> blastx_cline = NcbiblastxCommandline(blastx, query = infile, db = nr, evalue = 0.001, out = outfile)
>>> stdout, stderr = blastx_cline()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File     "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Application/__init__.py", line 443, in __call__
stdout_str, stderr_str)
Bio.Application.ApplicationError: Command '/Users/Priya/Documents/Python/ncbi-blast-2.2.26+/bin/blastx -out /Users/Priya/Documents/Python/Tutorials/opuntia_python_local.xml -query /Users/Priya/Documents/Python/Tutorials/opuntia.txt -db /Users/Priya/Documents/Python/ncbi-blast-2.2.26+/bin/nr.pal -evalue 0.001' returned non-zero exit status 2, 'BLAST Database error: No alias or index file found for protein database [/Users/Priya/Documents/Python/ncbi-blast-2.2.26+/bin/nr.pal] in search path [/Users/Priya::]'

I'm not sure how to change the path to point to the nr database that I downloaded, but I thought I pointed to it correctly, since I can run this code from the command line without any problems:

Priyas-iMac:~ Priya$ /Users/priya/Documents/Python/ncbi-blast-2.2.26+/bin/blastx -query /Users/priya/Documents/Python/Tutorials/opuntia.txt -db /Users/priya/Documents/Python/ncbi-blast-2.2.26+/bin/nr -out /Users/priya/Documents/Python/Tutorials/opuntia_local.xml -evalue 0.001 -outfmt 5

The above command line code creates an XML explosion result file, as you would expect.

Any help helping solve this problem using the Biopython NCBI command line tools would be greatly appreciated!

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2 answers

nr nr.pal. nr ( .pal) . pal . .ncbirc , :

[BLAST]
BLASTDB=/directory/path/to/blast/databases

. nr ( ) nr.

, , NcbiblastxCommandline, print blastx_cline. , , .

EDIT: http://www.biostars.org/ , , StackExchange.

+5

, , , db, , :

# In the code
-db /Users/Priya/Documents/Python/ncbi-blast-2.2.26+/bin/nr.pal

.

# From the command line
-db /Users/priya/Documents/Python/ncbi-blast-2.2.26+/bin/nr

nr 2, ".pal", .

+1

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