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run a tool from python

Hello,

I have a command that it is executed normally in a directory where we will generate our results, when we want to do it from linux it suffices to be in the directory "result" and run the command (perl -input .....). I want to run it from python.... I created my variable: cmd = perl input.... subprocess.cal (cmd, shell = true) except that here I am not in the directory where I have to generate my results, do you have a solution ?

sequence sequencing next-gen
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written by Nobody • Nobody

You are right that you need subprocess to run the command. You can either express your full paths in the command, or use os.chdir() to move to new folders.

If you're running a perl script from within python though, this strikes me as not the most efficient process.

I'm going to leave the post open for now, but note that this is not obviously a bioinformatics question so may be closed.

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written by Joe Joe

i knew i have to use os.chdir () but i dont know how to apply it. os.chdir (my path) and the line after I type my command and after my subprocess.call?

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written by Nobody • Nobody 
os.chdir(my path) \\
cmd = perl + pathBam + path... \\
subprocess.call(cmd, shell=true)
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updated by GenoMax GenoMax • written by Nobody • Nobody

How about:

cmd = 'cd <your directory> ; ' + perl + pathBam + path... \\
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written by Mensur Dlakic Mensur Dlakic

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