I am trying to a run a .exe file from python and pipe a string into it. The .exe itself opens a command box and requires a series of string inputs that can be entered in one go on a series of lines (as below)
In bash the solution would be:
printf "test.dat\nMoreinput\nMoreinput" | ~/Desktop/Median_filt_exes/ascxyz.exe
To recreate this in python I have tried:
from subprocess import Popen, PIPE
p = Popen(r"./ascxyz.exe", stdin=PIPE,text=True)
p.communicate("test.dat\nMoreinput/nMoreinput")
There's no error however it doesn't seem to be working (the .exe should create a new file when run successfully). Any help into what I could do to figure out why the exe isnt running properly would be very appreciated!
The immediate problem is probably that you are not terminating the input with a newline. But you really also don't want to do the Popen plumbing yourself.
from subprocess import run
run(['./ascxyz.exe'], text=True,
input="test.dat\nMoreInput\nMoreInput\n")
Notice also how we pass in a list as the first argument, to avoid the complications of shell=True.
Related
I've been attempting to execute a certain CLI from within python and store the output for later use within the same script. I suspect this question has a simple answer, but if one wishes to go through the entire pipeline, here is the tool in question.
wget http://rna.urmc.rochester.edu/Releases/current/RNAstructureForLinux.tgz
tar xvf as usual, go inside the resulting directory and execute 'make all', the executables I use in the bash script are within the 'exe' directory.
I attempted to execute the commands with os.system(), but with little luck. The CLI I am using; however, seems to be running. The function which I have set to execute the os.system() commands contains the following block.
txt = open('home/spectre/tools/RNAstructure/exe/RNAStructure_nucleic_acid.txt',"w")
txt.write('AAGGCTGTCCAGGCGCAATGTGGTGGCTGCTTCTCTGGGGAGTCCTCCAGGCTTGCCCAACCCGGGGCTCCGTCCTCTTGGCCCAAGAGCTACCCCAGCAGCTGACATCCCCCGGGTACCCAGAGCCGTATGGCAAAGGCCAAGAGAGCAGCACGGACATCAAGGCTCCAGAGGGCTTTGCTGTGAGGCTCGTCTTCCAGGACTTCGACCTGGAGCCGTCCCAGGACTGTGCAGGGGACTCTGTCACAGTGAGCTGGGGATGGGGGGGGTCCCGCCAGGACTGTGGCCAGGGAGATTCCCGGGGTTGTGGGAAGTGGCGGTGCCCTGAATCCCCCATCTGGAGGAGGGATGAAT')
os.system(' cd ~/tools/RNAstructure/exe ; ./python_RNA_structure.sh')
nucleotides, structure, MFE =
RNAStructure_from_file('home/spectre/tools/RNAstructure/exe/RNAStructure_bracket_output.txt')
The executable *.sh file contains this.
#!/bin/bash
cd ~/tools/RNAstructure/exe
./Fold RNAStructure_nucleic_acid.txt RNAStructure_nucleic_acid_output.txt
./ct2dot RNAStructure_nucleic_acid_output.txt -1 RNAStructure_bracket_output.txt
If I execute the bash script from the command line the output should look a little like this
Initializing nucleic acids...
Using auto-detected DATAPATH: "../data_tables" (set DATAPATH to avoid this warning).
done.
98% \[==================================================\] \\ done.
Writing output ct file...done.
Single strand folding complete.
Converting CT file...
Using auto-detected DATAPATH: "../data_tables" (set DATAPATH to avoid this warning).
CT file conversion complete.
If I execute the bash script form the python file.
Initializing nucleic acids...
Using auto-detected DATAPATH: "../data_tables" (set DATAPATH to avoid this warning).
Error reading sequence. The file did not contain any nucleotides.
Single strand folding complete with errors.
Converting CT file...
Using auto-detected DATAPATH: "../data_tables" (set DATAPATH to avoid this warning).
CT file conversion complete.
It looks an awful lot like my CLI can find the files it needs inside the terminal, but not outside of it. I haven't experimented with any parameters like trying absolute paths, but I understood by using os.system() I could execute a bash script, but it is not clear to me why this is changing how that script behaves.
What I've done to resolve the problem:
reopening the file seems to resolve the problem, but I am still working out why.
The problem seems to resolve when I reopen the file within the python script like so:
txt = open('home/spectre/tools/RNAstructure/exe/RNAStructure_nucleic_acid.txt',"w")
txt.write('AAGGCTGTCCAGGCGCAATGTGGTGGCTGCTTCTCTGGGGAGTCCTCCAGGCTTGCCCAACCCGGGGCTCCGTCCTCTTGGCCCAAGAGCTACCCCAGCAGCTGACATCCCCCGGGTACCCAGAGCCGTATGGCAAAGGCCAAGAGAGCAGCACGGACATCAAGGCTCCAGAGGGCTTTGCTGTGAGGCTCGTCTTCCAGGACTTCGACCTGGAGCCGTCCCAGGACTGTGCAGGGGACTCTGTCACAGTGAGCTGGGGATGGGGGGGGTCCCGCCAGGACTGTGGCCAGGGAGATTCCCGGGGTTGTGGGAAGTGGCGGTGCCCTGAATCCCCCATCTGGAGGAGGGATGAAT')
txt = open('home/spectre/tools/RNAstructure/exe/RNAStructure_nucleic_acid.txt')
os.system(' cd ~/tools/RNAstructure/exe ; ./python_RNA_structure.sh')
nucleotides, structure, MFE =
RNAStructure_from_file('home/spectre/tools/RNAstructure/exe/RNAStructure_bracket_output.txt')
I am not sure why this resolves the problem, I found this solution serendipitously. I'll update the answer when I figure out why, unless someone wants to beat me to it. It's magic to me for now.
It seems that after opening the file, RNAStructure_nucleic_acid.txt, and assigning it to the txt variable for writing, I need to reopen it after writing is complete. Otherwise the file is blank when I try printing it's output within the program, but after the program finishes executing, the file contains the correct text.
Hello all,
i'm looking for a way to execute a KNIME workflow in Python in batch mode (without opening the GUI of KNIME, https://www.knime.com/faq#q12)
After hours of trying I am asking you whether you can help me in this case:
When I run the python file, it opens the Knime exe, after some seconds the knime GUI is also opened. Unfortunately, the exe is not excuting the workflow (for testing the workflow should read an csv file and save it in another file destination)
This is actual code in python 3.7:
import subprocess
subprocess.run(["C:/Program Files/KNIME/knime.exe","-consoleLog","-nosplash","-noexit","-nosave","-reset","-application org.knime.product.KNIME_BATCH_APPLICATION","-workflowDir= C:/Users/jssch/knime-workspace/testexecute"]
When i paste the following code in command line the code is working and is executed correctly (it just hands over the arguments and does not open the knime GUI):
C:\Program Files\KNIME\knime.exe" -consoleLog -noexit -nosplash -nosave -reset -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir="C:\Users\jssch\knime-workspace\testexecute"
Thanks for your help in advance!
I think you made a mistake with the -application part, they should be in different Strings. Also the -workflowDir= C:/... seems to have an extra space too.
The problematic part:
"-application org.knime.product.KNIME_BATCH_APPLICATION"
it should be:
"-application", "org.knime.product.KNIME_BATCH_APPLICATION"
Probably you do not want the -noexit argument either.
All together:
import subprocess
subprocess.run(["C:/Program Files/KNIME/knime.exe", "-consoleLog", "-nosplash", "-nosave", "-reset", "-application", "org.knime.product.KNIME_BATCH_APPLICATION", "-workflowDir=C:/Users/jssch/knime-workspace/testexecute"]
(I usually prefer the paths without spaces, strange characters, I would use a KNIME installation from a different path, though this is fine too.)
I'm trying to read the duration of video files using mediainfo. This shell command works
mediainfo --Inform="Video;%Duration/String3%" file
and produces an output like
00:00:33.600
But when I try to run it in python with this line
subprocess.check_output(['mediainfo', '--Inform="Video;%Duration/String3%"', file])
the whole --Inform thing is ignored and I get the full mediainfo output instead.
Is there a way to see the command constructed by subprocess to see what's wrong?
Or can anybody just tell what's wrong?
Try:
subprocess.check_output(['mediainfo', '--Inform=Video;%Duration/String3%', file])
The " in your python string are likely passed on to mediainfo, which can't parse them and will ignore the option.
These kind of problems are often caused by shell commands requiring/swallowing various special characters. Quotes such as " are often removed by bash due to shell magic. In contrast, python does not require them for magic, and will thus replicate them the way you used them. Why would you use them if you wouldn't need them? (Well, d'uh, because bash makes you believe you need them).
For example, in bash I can do
$ dd of="foobar"
and it will write to a file named foobar, swallowing the quotes.
In python, if I do
subprocess.check_output(["dd", 'of="barfoo"', 'if=foobar'])
it will write to a file named "barfoo", keeping the quotes.
This question already has answers here:
how to direct output into a txt file in python in windows
(6 answers)
Closed 6 years ago.
I am running a python script which checks for the modifications of files in a folder. I want that output to be printed in a file. The problem is that the output is DYNAMIC , the cmd is always open and when a file is modified, I will have an information right-ahead about that in the cmd window. All the solutions which I found were matching the situations were I just run a command and I finish with that.
I tryed with:
python script.py > d:\output.txt but the output.txt file is empty
An example of the command prompt windows, after I run the command python script.py and I touch the 2 files, the command prompt will look like this. I want to capture that output.
Solution: In the python script which I use, add to the logging.basicConfig function, one more argument : filename='d:\test.log'
The issue is output buffering. If you wait long enough, you'll eventually see data show up in the file in "blocks". There are a few ways around it, for example:
Run python with the -u (unbuffered) flag
Add a sys.stdout.flush() after all print statements (which can be simplified by replacing stdout with a custom class to do it for you; see the linked question for more)
Add flush=True option to print statements if your version of Python supports it
If appropriate, use the logging module instead of print statements.
python test.py>test.txt
It's working for me in windows cmd prompt
As I see it the simplest would be to add the file handling (the writing to output.txt ) inside your script. Thus, when it is time to print the information you need to have (as your example shows when you touch two files you print two lines), you can open the file, write the specific line and close it after it is done (then you can see the updated output.txt).
Get the file path for the output.txt as a command line argument like
python script.py --o 'd:\output.txt'
for example.
I'm a win7-user.
I accidentally read about redirections (like command1 < infile > outfile) in *nix systems, and then I discovered that something similar can be done in Windows (link). And python is also can do something like this with pipes(?) or stdin/stdout(?).
I do not understand how this happens in Windows, so I have a question.
I use some kind of proprietary windows-program (.exe). This program is able to append data to a file.
For simplicity, let's assume that it is the equivalent of something like
while True:
f = open('textfile.txt','a')
f.write(repr(ctime()) + '\n')
f.close()
sleep(100)
The question:
Can I use this file (textfile.txt) as stdin?
I mean that the script (while it runs) should always (not once) handle all new data, ie
In the "never-ending cycle":
The program (.exe) writes something.
Python script captures the data and processes.
Could you please write how to do this in python, or maybe in win cmd/.bat or somehow else.
This is insanely cool thing. I want to learn how to do it! :D
If I am reading your question correctly then you want to pipe output from one command to another.
This is normally done as such:
cmd1 | cmd2
However, you say that your program only writes to files. I would double check the documentation to see if their isn't a way to get the command to write to stdout instead of a file.
If this is not possible then you can create what is known as a named pipe. It appears as a file on your filesystem, but is really just a buffer of data that can be written to and read from (the data is a stream and can only be read once). Meaning your program reading it will not finish until the program writing to the pipe stops writing and closes the "file". I don't have experience with named pipes on windows so you'll need to ask a new question for that. One down side of pipes is that they have a limited buffer size. So if there isn't a program reading data from the pipe then once the buffer is full the writing program won't be able to continue and just wait indefinitely until a program starts reading from the pipe.
An alternative is that on Unix there is a program called tail which can be set up to continuously monitor a file for changes and output any data as it is appended to the file (with a short delay.
tail --follow=textfile.txt --retry | mycmd
# wait for data to be appended to the file and output new data to mycmd
cmd1 >> textfile.txt # append output to file
One thing to note about this is that tail won't stop just because the first command has stopped writing to the file. tail will continue to listen to changes on that file forever or until mycmd stops listening to tail, or until tail is killed (or "sigint-ed").
This question has various answers on how to get a version of tail onto a windows machine.
import sys
sys.stdin = open('textfile.txt', 'r')
for line in sys.stdin:
process(line)
If the program writes to textfile.txt, you can't change that to redirect to stdin of your Python script unless you recompile the program to do so.
If you were to edit the program, you'd need to make it write to stdout, rather than a file on the filesystem. That way you can use the redirection operators to feed it into your Python script (in your case the | operator).
Assuming you can't do that, you could write a program that polls for changes on the text file, and consumes only the newly written data, by keeping track of how much it read the last time it was updated.
When you use < to direct the output of a file to a python script, that script receives that data on it's stdin stream.
Simply read from sys.stdin to get that data:
import sys
for line in sys.stdin:
# do something with line