The python subprocess module is a part of the standard python library that enables a user to run a variety of subprocess within python and collect their output and error pipes. It is a wonderfully handy tool that really expands the possibilities of what python is capable of doing. The tool is intended to build upon and essentially replace a lot of the functionality of the os package which I have found cumbersome to use. The main commands of the subprocess module include:
subprocess.call-runs a command and returns output and the exit code
subprocess.check_call-runs a command; if exit code is 0 returns output, otherwise CalledProcessError
Here are some simple example scripts to help get started using the subprocess inside python code:
A repository of programs, scripts, and tips essential to
genetic epidemiology, statistical genetics, and bioinformatics
Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.
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