na2aa

Convert DNA sequences to longest amino acide sequence for all six reading frames

Installation

I suppose you do not want to keep the package installed, thus I recommend to install it in a fresh virtual environment.

Clone the repository then change into the directory and execute:

pip install .

Usage

na2aa -s <sequences.fasta> -i <intervals.gff> -c <standard_code.txt>

Example

In the example folder, run:

na2aa -s sequences.fasta -i intervals.gff -c standard_code.txt

The output is printed to the command line but you can find the example output also in the file genes.fasta.

Issues

• input formats should be exactly the same format as in the example
• slightly different results possible depending on whether start and stop are inclusive or exclusive and if the intervals are zero or one-based
• start codon not properly implemented

Future Development

• this is just a small showcase project