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A simple python program to split MSAs in FASTA format.
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Changed Jenkins pipeline to use mamba
2023-04-11 13:00:04 -05:00
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splitmsa Renamed project to "SplitMSA" and added pipeline file 2023-04-11 12:39:04 -05:00
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README.md Renamed project to "SplitMSA" and added pipeline file 2023-04-11 12:39:04 -05:00
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README.md

SplitMSA

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