Sequence Translation

Translate nucleotide sequences to amino acid sequences. For available translation tables, see CLI translation guideline. Note that the translation table is in a string format, not an integer.

Steps

Install PySEGUL using pip if you haven't done it yet

pip install pysegul

Create a new Python script, import the library, and write python code

import pysegul

def translate_sequences():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    table = '1'
    # Set reading frame to 1, 2, or 3
    reading_frame = 1
    output_dir = 'tests/output'
    translate = pysegul.SequenceTranslation(
        input_format,  
        datatype, 
        output_dir, 
        output_format,
        table,
        reading_frame
        )
    translate.from_dir(input_dir)

You can also input the alignment paths in a list directly instead of using a directory. Replace the input_dir with input_files and provide a list of paths. Then, call the from_files method instead of from_dir.

import pysegul

def translate_sequences():
    input_path = ['tests/align-data/alignment1.nex', 'tests/align-data/alignment2.nex']
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    table = '1'
    reading_frame = 1
    output_dir = 'tests/output'
    translate = pysegul.SequenceTranslation(
        input_format,  
        datatype, 
        output_dir, 
        output_format,
        table,
        reading_frame
        )
    translate.from_files(input_path)