Dependencies

This script needs the biogl module to function properly. If you use (or can get) pip, you can simply do

python3 -m pip install biogl

to add the package to a location reachable by your Python installation.

Otherwise, you can clone the biogl repo and source it locally (to run from anywhere, you'll need to add it to your PYTHONPATH environment variable, a process that varies by OS):

git clone https://github.com/glarue/biogl.git

Usage info

usage: transeq [-h] [-v {short,long}] [-p {1,2}] [-r] [-s STOP_CHARACTER]
               [--no_mask] [--keep_whitespace]
               [sequence_input]

Translate nucleotide sequence into amino acid sequence

positional arguments:
  sequence_input        sequence string or file containing sequence(s)
                        (default: None)

optional arguments:
  -h, --help            show this help message and exit
  -v {short,long}, --verbosity {short,long}
                        amino acid abbreviation length (e.g. Glu/Glutamine)
                        (default: single)
  -p {1,2}, --phase {1,2}
                        change the phase of translation (default: 0)
  -r, --reverse_complement
                        reverse-complement the sequence before translation
                        (default: False)
  -s STOP_CHARACTER, --stop_character STOP_CHARACTER
                        the string to use for stop codons (default: *)
  --no_mask             do not mask unrecognized codons with X; report
                        lowercased (default: False)
  --keep_whitespace, -k
                        treat whitespace (both bordering and internal) as
                        sequence (default: False)