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Python scripts

This is the home page for a collection of Python scripts provided to assist in processing data for UPARSE and other multi-step pipelines.

Python scripts index.

Download python_scripts.tar.gz. Create a new directory for the scripts, change to that directory and extract the tarball. E.g. if you downloaded python_scripts.tar.gz into your home directory (~), then you could create a directory called drive5_py for the scripts, like this:

mkdir ~/drive5_py
cd ~/drive5_py
tar -zxvf ~/python_scripts.tar.gz

Running a script
The simplest way to run a script is to type python followed by the path name of the script and the arguments required by the script. Usually the first command-line agument for the script is the input filename, and most scripts write to standard output, which you can capture into a file by using > filename. Assuming you installed the scripts in ~/drive5_py, then a typical command to execute a script looks like like this:

python ~/drive5_py/script_name.py input_file_name > output_file_name