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Python Subprocess Windows The System Cannot Find The File Specified

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I have done this in other cases with os.startfile and other cases and would like to fix it. See the warning under Frequently Used Arguments for details. Biopython NCBIcommandline from PHP Hi, this is my first post.  I am writing a web program in PHP and I want it to perform a python s... If cmd is a list of arguments, like the example above, you should use subprocess.Popen(cmd,...) (like the example above, too). http://rss4medics.com/cannot-find/python-the-system-cannot-find-the-file-specified-subprocess.php

That will quickly fill the buffer available in the pipe between you and the subprocess, and the subprocess will block. Thanks, Niek Edit: I used blast 2.2.17 in command line directly (using same commands as used above) to create an xml file and read that in as result_handle. Therefore, you should modify your example to explicitly invoke git.cmd So to workaround this issue, all I did is edit the subprocess.py file and convert "git" to "git.cmd" in the args ADD REPLY • link written 6.0 years ago by Niek De Klein • 2.3k Can you update your code to the one you are using with 2.2.24+ and paste the print http://stackoverflow.com/questions/3022013/windows-cant-find-the-file-on-subprocess-call

File Line 958, In _execute_child Startupinfo)

if I do it in a batch file the output file is spaced correctly.. Perl Browse more Python Questions on Bytes Question stats viewed: 3968 replies: 3 date asked: Mar 17 '06 Follow this discussion BYTES.COM 2016 Formerly "TheScripts.com" from 2005-2008 About Bytes | If cmd is a list of arguments, like the example above, you should usesubprocess.Popen(cmd,...) (like the example above, too). if I do it in a batch file the output file is spaced correctly..

If the BLAST+ binaries are not on the $PATH environment variable (which is probably the case on Windows unless you set this up yourself), you'll get the observed error: WindowsError: [Error You are waiting for your subprocess to complete without reading away what it prints. Join them; it only takes a minute: Sign up Cannot find the file specified when using subprocess.call('dir', shell=True) in Python up vote 12 down vote favorite 1 In a 64-bit system Python Subprocess Windows Error 2 GO OUT AND VOTE What is this line of counties voting for the Democratic party in the 2016 elections?

If cmd is a list of arguments, like the example above, you should use subprocess.Popen(cmd,...) (like the example above, too). Python Filenotfounderror: [winerror 2] The System Cannot Find The File Specified Would we find alien music meaningful? I updated the question... –Andreas Dec 2 '13 at 14:34 Are you running the script from console or from some IDE? –Fenikso Dec 2 '13 at 14:45 1 ADD COMMENT • link written 6.0 years ago by Istvan Albert ♦♦ 66k 1 6.0 years ago by Michael Schubert • 6.6k Cambridge, UK Michael Schubert • 6.6k wrote: I'm still

seems like more work than I should have to do to use options with a command line program.. Python The System Cannot Find The Path Specified bellman @ lysator.liu.se only proved it correct, not tried it." ! python is working corectly then. Stani --http://pythonide.stani.be- Hide quoted text - - Show quoted text - evedently when they converted awk from unix to windows (gawk) they left the formating the same..

Python Filenotfounderror: [winerror 2] The System Cannot Find The File Specified

Python 3.x latest, stable. What does "there lived here then" mean? File Line 958, In _execute_child Startupinfo) Printing it line by line? Python Subprocess.popen Cannot Find File Which is what you would expect if it works in the shell.

dir ...it of course prints the present folder content. check my blog the-shank commented Jun 12, 2014 I dug into this further and from this post on StackOverflow, I found the solution. They are found by the operating system, though, at least when run on the command prompt. Try print repr(your_data) to see exactly what you got. -- Gabriel Genellina Did you take in account that line endings on Windows are '\r\n' and not '\n'? Pytesseract Filenotfounderror: [winerror 2] The System Cannot Find The File Specified

msg101667 - (view) Author: STINNER Victor (haypo) * Date: 2010-03-25 01:49 Oops. You do not need shell=True to run a batch file or console-based executable. Can Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline so that no .xml file is created? http://rss4medics.com/cannot-find/python-subprocess-windows-cannot-find-the-file-specified.php C# TBB updating metadata value What is a satisfactory result of penetration testing assessment?

Terms Privacy Security Status Help You can't perform that action at this time. Python Subprocess No Such File Or Directory from Bio.Blast import NCBIStandalone from Bio.Blast import NCBIXML my_blast_db = r"C:\Niek\Test2.2.17\Worm\c_elegans.protein.WS200.fasta" my_blast_file = r"C:\Niek\Test2.2.17\Worm\worm-HD.fasta" my_blast_exe = r"C:\Niek\blast-2.2.17\bin\blastall.exe" result_handle, error_handle = NCBIStandalone.blastall(my_blast_exe, "blastp", my_blast_db, my_blast_file, matrix="BLOSUM62") blast_records = NCBIXML.parse(result_handle) y = 0 What do you get with print repr(cmd)?

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Why not use os.listdir() instead? –Martijn Pieters♦ Dec 2 '13 at 14:17 strange, the code works for me on ubuntu, rhel, win xp, win 7 –alko Dec 2 '13 The second example uses BLAST+ (the current version of NCBI BLAST), but has a problem: from Bio.Blast.Applications import NcbiblastpCommandline my_blast_db = r"C:\Niek\Test2.2.17\Worm\c_elegans.protein.WS200.fasta" my_blast_file = r"C:\Niek\Test2.2.17\Worm\worm-HD.fasta" blastp_cline = NcbiblastpCommandline(cmd='blastp', query=my_blast_file, db=my_blast_db, evalue=0.01, Reload to refresh your session. Returned Non-zero Exit Status 1 import subprocess from os import system cmd = """gawk -f altertime.awk -v time_offset=4 -v outfile="testdat.sco" "i1.sco" """ #subprocess.Popen.

Hi, I would like parse the XML output of a local psiblast (NcbipsiblastCommandline wrapper) by pu... I'm trying to replace os.system() in bitbucket.org/srirangan/opendevice/src/tip/tools/net/srirang‌an/… to subprocess.call() –Sri Jun 11 '10 at 10:35 | show 1 more comment 4 Answers 4 active oldest votes up vote 75 down vote I had cut and pasted the example in to get that error... http://rss4medics.com/cannot-find/python-the-system-cannot-find-the-path-specified.php Should I allow my child to make an alternate meal if they do not like anything served at mealtime?