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POBiopython error - The system cannot find the file specified
 

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  1. POBiopython error - The system cannot find the file specified
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    <p>I have encountered an error which I am not able to resolve.</p> <p>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. </p> <p>The code looks as following:</p> <pre><code>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() </code></pre> <p>And the error I get:</p> <pre><code> File "C:\Users\IBM_ADMIN\Desktop\PYTHON\Workspace\Biopython\blast.py", line 20, in &lt;module&gt; 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 </code></pre> <p>I am using:</p> <ul> <li>Eclipse SDK Version: 3.7.1</li> <li>Python version 2.7</li> <li>OS: 64 bit Windows 7</li> </ul> <p>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.</p> <p>Does anybody know how to fix this error?</p>
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    1. CODoes BioPython need any dependencies, e.g. some installation for BLAST support? Double-check it. It looks very much like the application startup code wants to start some native process (thus `subprocess.py`) and cannot find the executable.
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    2. COHave you installed 'blastn', included with blast+? http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download Biopython calls the native program, so that needs to be installed and on your path.
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    3. COBrad: Your solution works. Thank you so much !
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