Module xi_covutils.xi_covutils_app
XI Cov Utils - Command line interface
Expand source code
#!/usr/bin/env python
"""
XI Cov Utils - Command line interface
"""
import warnings
import click
from Bio import BiopythonDeprecationWarning
from xi_covutils.primers.infer import (
count_matches, guess, inspect, mismatch_histogram
)
with warnings.catch_warnings():
warnings.simplefilter(
action="ignore",
category=BiopythonDeprecationWarning
)
from xi_covutils.conservation import calculate_conservation, conservation_plot
from xi_covutils.msa import compare_msas
VERSION = "0.7.0"
@click.group()
def cli():
"""Main group of CLI commands
"""
click.echo(f"# XI - Cov Utils {VERSION}")
@click.group()
def msa():
"""
MSA commands group
"""
msa.add_command(calculate_conservation)
msa.add_command(conservation_plot)
msa.add_command(compare_msas)
@click.group()
def seqs():
"""
Sequence commands.
"""
cli.add_command(msa)
cli.add_command(seqs)
seqs.add_command(guess)
seqs.add_command(inspect)
seqs.add_command(count_matches)
seqs.add_command(mismatch_histogram)
if __name__ == "__main__":
cli()