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sequence-analysis

Programs for analyzing biological sequences such as DNA, RNA, and proteins.

This project currently implements Needleman-Wunsch and Waterman-Smith-Beyer algorithms for pairwise sequence alignment.

Reports are generated using Sphinx Doc.

Prerequisites

  • Python 3
  • Linux (might work elsewhere too)
  • LaTeX (optional if building PDFs is needed)

Usage

Optionally, everything can be run within the binftools container (separate project) which provides all prerequisites listed above. Just mount this project within the container and get to work.

$ cd sequence-analysis
$ docker run -it --rm -v "$(pwd):/sequence-analysis" ajsmith/binftools bash
[me@22922011bda7 ~]$ cd /sequence-analysis

To install (this will create and install everything into a Python virtualenv):

$ ./install.sh

To run the tests and code quality checks:

$ ./run-tests.sh

For algorithms, please see the doc: https://github.com/ajsmith/sequence-analysis/blob/main/hw1/source/index.rst

For tests, see the "tests/" directory.