I have encountered an error which I am not able to resolve.
I am trying to perform the easiest set of commands that will perform a tBLASTn algorithm, looking for a sequence (sequence specified as a "pytanie.fasta" file) in a database (also specified as file -> cucumber.fasta). The result will be saved in the "wynik.txt" file.
The code looks as following:
from Bio.Blast. Applications import NcbitblastnCommandline
database = r"\Biopython\cucumber.fasta"
qr = r"\Biopython\pytanie.fasta"
output = r"\Biopython\wynik.txt"
e = raw_input("Enter e-value: ")
tblastn_cline = NcbitblastnCommandline(cmd='blastn', db=database, query=qr, out=output, evalue=e, outfmt=7)
print tblastn_cline
stdout, stderr = tblastn_cline()
And the error I get:
File "C:\Users\IBM_ADMIN\Desktop\PYTHON\Workspace\Biopython\blast.py", line 20, in <module>
stdout, stderr = tblastn_cline()
File "C:\Python27\lib\site-packages\Bio\Application\__init__.py", line 435, in __call__
shell=(sys.platform!="win32"))
File "C:\Python27\lib\subprocess.py", line 679, in __init__
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 893, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
I am using:
- Eclipse SDK Version: 3.7.1
- Python version 2.7
- OS: 64 bit Windows 7
I have tried this also on 32-bit Windows XP and it produces the same error. Biopython package should work fine since it went through the tests suggested by biopython website. I have also tried other formats of the path where the files are located, but it did not work. My friend uses the same code on Ubuntu and it works fine.
Does anybody know how to fix this error?
