Alignment Conversion

Convert an alignment from one format to another format. Optimized for converting many alignments in parallel without the limitation for Python’s GIL.

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 convert_alignments():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    sort_sequences = True
    output_dir = 'tests/output'
    convert = pysegul.AlignmentConversion(
        input_format,
        datatype,
        output_dir,
        output_format,
        sort_sequences
        )
    convert.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 convert_alignments():
    input_path = ['tests/align-data/alignment1.nex', 'tests/align-data/alignment2.nex']
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    sort_sequences = True
    output_dir = 'tests/output'
    convert = pysegul.AlignmentConversion(
        input_format,
        datatype,
        output_dir,
        output_format,
        sort_sequences
        )
    convert.from_files(input_path)