#!/usr/bin/env python

import logging
import subprocess
from Bio import SeqIO


def make_parsnp_tree(fasta_files, reference_fasta=None, logfile=None):
    """
    For this one - get a list of fasta files, and then run parsnp
    :param fasta_files:
    :param reference_fasta:
    :return:
    """
    pass


def make_gene_tree(fasta_file, logfile=None):
    pass


def make_multigene_tree(fasta_files, logfile=None):
    pass
