/bioinf_tools

Primary LanguagePython

Simple bioinformatic tools

Routine tools and a template for future projects.

The plan is to add custom scripts for various tasks here. This will update an old repo I had that was similar in purpose but is now deprecated.

Tools by type and their usage:

Basic string tools

  • count_nuc - counts the number of times each nucleotide occurs in a string. (count_nuc -s STRING)
  • rev_comp - returns the reverse complement of a string. (rev_comp -i STRING)
  • gc_content - returns the GC content of a string. (function in seq_tools)
  • sliding_window - returns GC content of string over sliding window. (function in seq_tools)

Conversion and IO tools

  • parquet_converter - convert a parquet file to a csv. (-input, -i, path)

Installation

After cloning this repo, navigate into it and type: pip install ./