Alignment Summary

Generate summary statistics for DNA and amino acid alignments.

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 summarize_alignments():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    # Available values for interval: 1, 2, 5, 10.
    completeness_interval = 5
    prefix = 'concatenated'
    output_dir = 'tests/output'
    concat = pysegul.AlignmentSummary(
        input_format,
        datatype,
        output_dir,
        completeness_interval,
        prefix
        )
    concat.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 summarize_alignments():
    input_path = ['tests/align-data/alignment1.nex', 'tests/align-data/alignment2.nex']
    input_format = 'nexus'
    datatype = 'dna'
    completeness_interval = 5
    prefix = 'concatenated'
    output_dir = 'tests/output'
    concat = pysegul.AlignmentSummary(
        input_format,
        datatype,
        output_dir,
        completeness_interval,
        prefix
        )
    concat.from_files(input_path)

Per-locus summary

Upcoming

The per_locus option is not yet published on PyPI. It will be available in the next PySEGUL release. To use it now, build PySEGUL from source.

Set per_locus to True to write a summary for each alignment instead of one summary across all alignments:

summary = pysegul.AlignmentSummary(
    'nexus',
    'dna',
    'tests/output',
    5,
    per_locus=True,
    )
summary.from_dir('tests/align-data')