2023-03-22 19:30:53 +00:00
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# MSA Splitter
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Simple FASTA file splitter. Capable of batch trimming a large amount of sequences in the form of a MSA in a FASTA file.
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2023-03-22 20:13:37 +00:00
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## Features
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- Split large fasta files that contain a multiple sequence alignment (MSA) into individual genes
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- Trim off stop codon
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- Batch process multiple genes from one MSA
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- Correct gene start and stop locations based on start and stop codon location
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- Catalogues errors that occurred in human-readable CSV file
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## Planned
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- Translate MSA into amino acids while maintaining alignment (shows type of mutation if frameshift)
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- Simple to use GUI
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- Run without system-wide python install
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## Use
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### Command Line
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1. Install python 3
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2. Install `biopython`
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- Using `pip`: `pip install biopython` or `pip3 install biopython`
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- Using `conda`: ` conda install -c conda-forge biopython`
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3. Download `msa_splitter.py` and run with `python3 msa_splitter.py`
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- `python3 msa_splitter.py -h` for help
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