A collection of useful scripts for computational biology.

Intended to be used for computation biology projects (e.g. based on this template).

Scripts should be well documented.

• Required: Each script has a docstring (comment at the top after the shebang) which describes the use of the script from the command line.
• Good: Scripts are well commented, explaining the logic of any difficult to understand code.
• Great: Scripts are designed with full help text, conforming to POSIX standards.

Scripts should take any data which only needs to be used once from STDIN. If this can be accomplished in multiple ways, one rule of thumb is for scripts to take the largest files (usually a sequence file) from STDIN and smaller metadata files as positional arguments. This is designed to make streaming pipelines an easy transition.

Scripts should be designed for portability.

• Good: Scripts accept all input data externally. Data files are not hard coded into the script.
• Great: Variable parameters of the analysis are accepted as positional arguments, and options. Logical defaults are acceptable. Parameters are not hard-coded into the scripts.
• Greatest: Scripts are constructed in a modular design. e.g. Python scripts divide logical chunks into "public" functions so that those parts can be imported by other scripts.