Hi I'm trying to execute bash command in python by importing commands module.I think I ask the same question here before. However this time it doesn't work.
The script is as below:
#!/usr/bin/python
import os,sys
import commands
import glob
path= '/home/xxx/nearline/bamfiles'
bamfiles = glob.glob(path + '/*.bam')
for bamfile in bamfiles:
fullpath = os.path.join(path,bamfile)
txtfile = commands.getoutput('/share/bin/samtools/samtools ' + 'view '+ fullpath)
line=txtfile.readlines()
print line
this samtools view will produce (I think) .txt file
I got the errors:
Traceback (most recent call last):
File "./try.py", line 12, in ?
txtfile = commands.getoutput('/share/bin/samtools/samtools ' + 'view '+ fullpath)
File "/usr/lib64/python2.4/commands.py", line 44, in getoutput
return getstatusoutput(cmd)[1]
File "/usr/lib64/python2.4/commands.py", line 54, in getstatusoutput
text = pipe.read()
SystemError: Objects/stringobject.c:3518: bad argument to internal function
Seems it's the problem with commands.getoutput
Thanks
I would recommend using subprocess
From the commands documentation:
Deprecated since version 2.6: The commands module has been removed in Python 3.0. Use the subprocess module instead.
Update: Just realized you're using Python 2.4. An easy way to execute a command is os.system()
A quick google search for "SystemError: Objects/stringobject.c:3518: bad argument to internal function" brings up several bug reports. Such as https://www.mercurial-scm.org/bts/issue1225 and http://www.modpython.org/pipermail/mod_python/2007-June/023852.html. It appears to be an issue with Fedora in combination with Python 2.4, but I am not exactly sure about that. I would suggest that you follow Michael's advice and use os.system or os.popen to accomplish this task. To do this the changes in your code will be:
import os,sys
import glob
path= '/home/xxx/nearline/bamfiles'
bamfiles = glob.glob(path + '/*.bam')
for bamfile in bamfiles:
fullpath = os.path.join(path,bamfile)
txtfile = os.popen('/share/bin/samtools/samtools ' + 'view '+ fullpath)
line=txtfile.readlines()
print line
Related
I am trying to create a python def to unzip a few .gz files within a folder. I know that the main script works if it is not in the def. The script I have created is similar to others I have done but this one give me the error
File "unzip.py", line 24, in
decompressed_files(input_folder)
NameError: name 'input_folder' is not defined
I copied the script below so someone can help me to see where the error is. I haven't done any BioInformatics for the last couple of years and I am a bit rusty.
import glob
import sys
import os
import argparse
import subprocess
import gzip
def decompressed_files(input_folder):
print ('starting decompressed_files')
output_folder=input_folder + '/fasta_files'
if os.path.exists(output_folder):
print ('folder already exists')
else:
os.makedirs(output_folder)
for f in input_folder:
fastqs=glob.glob(input_folder + '/*.fastq.gz')
cmd =[gunzip, -k, fastqs, output_folder]
my_file=subprocess.Popen(cmd)
my_file.wait
print ('The programme has finished doing its job')
decompressed_files(input_folder)
This is done for python 2.7, I know that is old but it is the one that it is installed in my work server.
That's why when you call decompressed_files(input_folder) in the last line, you didn't define input_folder before. you should do it like this :
input_folder = 'C:/Some Address/'
decompressed_files(input_folder)
I am trying to find a specific pathname and pass this into os.chdir so I can run a command in that directory. I won't know the exact pathname hence why I have to run the find command. I have tried several ways to do this and each comes with a new error. The code below is one of the ways I have tried, can anyone suggest the best way to do this? Or how to fix this error?
Source Code:
import os
import subprocess
os.system('find ~ -path "*MyDir" > MyDir.txt')
output = subprocess.check_output("cat MyDir.txt", shell=True)
os.chdir(output)
os.system("file * > MyDir/File.txt")
The error:
Traceback (most recent call last):
File "sub1.py", line 8, in <module>
os.chdir(output)
FileNotFoundError: [Errno 2] No such file or directory: b'/Users/MyhomeDir/Desktop/MyDir\n'
I know that directory exists and presume it has something to do with the b' and \n'. I just don't know what the problem is.
Get rid of the \n with strip:
output = subprocess.check_output("cat MyDir.txt", shell=True).strip()
os.chdir(output)
How to know which file is calling which file in filesystem, like file1.exe is calling file2.exe
so file2.exe is modified,
and file1.exe is entered in log file.
winos
I have searched INTERNET but not able to find any samples.
In order know which file is calling which file you can use the Trace module
exp: if you have 2 files
***file1.py***
import file2
def call1():
file2.call2()
***file2.py***
def call2():
print "---------"
u can use it using console:
$ python -m trace --trackcalls path/to/file1.py
or within a program using a Trace object
****tracefile.py***
import trace,sys
from file1 import call1
#specify what to trace here
tracer = trace.Trace(ignoredirs=[sys.prefix, sys.exec_prefix], trace=0, count=1)
tracer.runfunc(call1) #call the function call1 in fille1
results = tracer.results()
results.write_results(summary=True, coverdir='.')
I am trying to setup a program where when someone enters a command it will run that command which is a script in a sub folder called "lib".
Here is my code:
import os
while 1:
cmd = input(' >: ')
for file in os.listdir('lib'):
if file.endswith('.py'):
try:
os.system(str(cmd + '.py'))
except FileNotFoundError:
print('Command Not Found.')
I have a file: lib/new_user.py But when I try to run it I get this error:
Traceback (most recent call last):
File "C:/Users/Daniel/Desktop/Wasm/Exec.py", line 8, in <module>
exec(str(cmd + '.py'))
File "<string>", line 1, in <module>
NameError: name 'new_user' is not defined
Does anyone know a way around this? I would prefer if the script would be able to be executed under the same window so it doesn't open a completely new one up to run the code there. This may be a really Noob question but I have not been able to find anything on this.
Thanks,
Daniel Alexander
os.system(os.path.join('lib', cmd + '.py'))
You're invoking new_user.py but it is not in the current directory. You need to construct lib/new_user.py.
(I'm not sure what any of this has to do with windows.)
However, a better approach for executing Python code from Python is making them into modules and using import:
import importlib
cmd_module = importlib.import_module(cmd, 'lib')
cmd_module.execute()
(Assuming you have a function execute defined in lib/new_user.py)
I am working on managing Canonical CM Landscape through Python api's. I don't know if any one could help me but am stuck in one point and I don't know if it is a simple Python error of that specific library. This is part of larger script but it drops when I tried to use the last function in this listing.
import os, json, sys, subprocess, csv, datetime, time
from landscape_api.base import API, HTTPError
from subprocess import Popen,PIPE,STDOUT,call
uri = "xxxxxxxxxxxxxxxxxxxxxxxx"
key = "xxxxxxxxxxxxxxxxxxxx"
secret = "xxxxxxxxxxxxxxxxxxxxxxx"
api = API(uri, key, secret)
proc=Popen('zenity --entry --text "Fill with machine Tag to be searched" --entry- text "Type Tag"', shell=True, stdout=PIPE, ) #Input from zenity window
output=proc.communicate()[0]
user="root"
script="2408"
mac = api.execute_script(query="tag:%s", script_id="script_id:%s", username="user:%s" %(output, script, user))
Last function api.execute_script returns error
Traceback (most recent call last):
File "Python_MAC_IP.py", line 35, in <module>
mac = api.execute_script(query="tag:%s", script_id="script_id:%s", username="user:%s" %(output, script, user))
TypeError: not all arguments converted during string formatting
You can only use the % operator on a single string, not across multiple strings. What you are currently asking Python to do is insert multiple variables into a string that only has one defined.
Change this line:
mac = api.execute_script(query="tag:%s", script_id="script_id:%s", username="user:%s" %(output, script, user))
to this:
mac = api.execute_script(query="tag:%s" %tag, script_id="script_id:%s" %script, username="user:%s" %user