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A simple python program to split MSAs in FASTA format.
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Python 95.2%
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Harrison Deng 89cde939b0 Added problem cataloging.
2023-03-22 15:13:37 -05:00
.gitignore Initial commit. 2023-03-22 14:30:53 -05:00
msa_splitter.py Added problem cataloging. 2023-03-22 15:13:37 -05:00
README.md Added problem cataloging. 2023-03-22 15:13:37 -05:00
requirements.txt Initial commit. 2023-03-22 14:30:53 -05:00

README.md

MSA Splitter

Simple FASTA file splitter. Capable of batch trimming a large amount of sequences in the form of a MSA in a FASTA file.

Features

  • Split large fasta files that contain a multiple sequence alignment (MSA) into individual genes
  • Trim off stop codon
  • Batch process multiple genes from one MSA
  • Correct gene start and stop locations based on start and stop codon location
  • Catalogues errors that occurred in human-readable CSV file

Planned

  • Translate MSA into amino acids while maintaining alignment (shows type of mutation if frameshift)
  • Simple to use GUI
  • Run without system-wide python install

Use

Command Line

  1. Install python 3
  2. Install biopython
    • Using pip: pip install biopython or pip3 install biopython
    • Using conda: conda install -c conda-forge biopython
  3. Download msa_splitter.py and run with python3 msa_splitter.py
    • python3 msa_splitter.py -h for help