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BLASTp query/options error Hello everyone, I am performing standalone blastp, I already used these commands on windows but ... python share|improve this question asked Nov 18 '13 at 7:57 Parseltongue 1,84094379 add a comment| 2 Answers 2 active oldest votes up vote 3 down vote accepted Specify program and its msg101647 - (view) Author: Sridhar Ratnakumar (srid) Date: 2010-03-24 18:26 Note that typing "foo.bar" in the Windows command line works, only subprocess is not able to find the executable. Why is looping over find's output bad practice? Continued
When I run the code however, a cmd/DOS window is opened, text is spit out, and it closes so fast I can not read the message and the map service it Pyro4+stackless How To Send Back Data/commands? However, I'm having a problem with the cmd. I see that Manipula.exe is running in the background, but it just hangs indefinitely.
E.g. Additionally, Linux does not suffer from this problem: $ python --version Python 2.7.3 $ cat test/script.sh #!/bin/sh echo "hello" $ PATH=$PATH:test script.sh hello $ PATH=$PATH:test python -c "from subprocess import call; Register Lostyourlogin? Python Subprocess Windows Error 2 Popen("foo") results in the same cannot find file error for me if the file is foo.bat.
How do I make an alien technology feel alien? Python Filenotfounderror: [winerror 2] The System Cannot Find The File Specified Is this what you were refering to in your #2 above? bellman @ lysator.liu.se only proved it correct, not tried it." ! check my blog Administration User List Committer List Help Tracker Documentation Tracker Development Report Tracker Problem Issue8224 classification Title: subprocess.Popen raises WindowsError if there is a dot in program name Type: behavior Stage: resolved
Currently it sea... Python The System Cannot Find The Path Specified In it, you'll get: The week's top questions and answers Important community announcements Questions that need answers see an example newsletter Linked 1 Can't make django less work on Windows 0 I have a hugh problem and I need to came out with the solution as soon as I can. about • faq • rss Community Log In Sign Up Add New Post Question: Windows Cmd Not Responding With Python Blastall 2.2.17 0 6.0 years ago by Niek De Klein •
dir ...it of course prints the present folder content. This is for Opendevice - an open source project to convert HTML5 apps into device specific apps. File Line 958, In _execute_child Startupinfo) blast against genomes in biopython from Bio import Entrez, SeqIO from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW result... Python Subprocess.popen Cannot Find File Browse other questions tagged python shell python-2.7 path subprocess or ask your own question.
share|improve this answer answered Nov 18 '13 at 7:59 Martijn Pieters♦ 507k7513351488 Thank you for the response. check my blog If I run it from the command line, Manipula will run for three seconds, do the necessary processing, and end itself. –Parseltongue Nov 18 '13 at 8:17 | show 7 more 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 But "subprocess.Popen(['foo.bar'])" will throw the following exception: Traceback (most recent call last): [...] File "C:\Python26\lib\subprocess.py", line 483, in check_call retcode = call(*popenargs, **kwargs) File "C:\Python26\lib\subprocess.py", line 470, in call return Popen(*popenargs, Pytesseract Filenotfounderror: [winerror 2] The System Cannot Find The File Specified
BLASTp in python (solved) I'm having some problems when running BLAST+ blastp from python. On Windows, the 'git' command is really installed as git.cmd. Reference Sheets Code Snippets C Snippets C++ Snippets Java Snippets Visual Basic Snippets C# Snippets VB.NET Snippets ASP.NET Snippets PHP Snippets Python Snippets Ruby Snippets ColdFusion Snippets SQL Snippets Assembly Snippets this content How do I avoid referring to all state variables when updating only a few?
Ballpark salary equivalent today of "healthcare benefits" in the US? Python Subprocess No Such File Or Directory But for other ArcGIS Server 10.0 python users that may stumble on this forum, I though I would send a code update for what worked. Not the answer you're looking for?
Is there still a way to prevent Trump from becoming president? Browse other questions tagged python path python-3.x or ask your own question. bambooom referenced this issue in bambooom/OMOOC2py Nov 17, 2015 Open [5w]MyDiarySAE #11 Soobrakay commented Sep 10, 2016 New version of git for windows (I have 2.9.3) installs git.exe instead of git.cmd, Returned Non-zero Exit Status 1 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,
Python 3.4, Biopython 1.65: Writing to file both subject and query IDs from parsed BLAST output I've performed a nucleotide BLAST of a multi-fasta file against itself in order to find share|improve this answer edited Jan 6 '13 at 4:28 Tian He 9711 answered Jan 6 '11 at 16:00 Douglas Macdonald 77463 8 That's because there's no executable called dir.exe while That will quickly fill the buffer available in the pipe between you and the subprocess, and the subprocess will block. have a peek at these guys Today's Topics Dream.In.Code > Programming Help > Python Need help using subprocess.Popen to run external command Page 1 of 1 New Topic/Question Reply 9 Replies - 8578 Views - Last Post:
David Murray (r.david.murray) * Date: 2010-03-25 02:06 In order to do that someone will need to confirm that this affects all versions of windows, and whether or not it is a I wanted to write: "This issue might be documented in subprocess documentation" :-/ msg101669 - (view) Author: R. Reload to refresh your session.