<commit_before>#!/usr/bin/env python
"""Module to split multiple sequence alignments of two taxa into separate MSAs per taxon."""

from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
from divergence import parse_options, extract_archive_of_files, create_directory, create_archive_of_files
import logging as log
import os.path
import shutil
import sys
import tempfile

def split_alignment_by_taxon(run_dir, genome_ids_a, genome_ids_b, sico_files):
    """Separate multiple sequence alignments with sequences from two taxa out into separate files per taxon."""
    #Collections to hold split files
    taxon_a_files = []
    taxon_b_files = []<commit_msg>Update run_codeml tool configuration to reflect changes in calling run_codeml Add TODO item to remove split_by_taxon after the above change is made final<commit_after>#!/usr/bin/env python
"""Module to split multiple sequence alignments of two taxa into separate MSAs per taxon."""

from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
from divergence import parse_options, extract_archive_of_files, create_directory, create_archive_of_files
import logging as log
import os.path
import shutil
import sys
import tempfile

#TODO Remove module & XML file

def split_alignment_by_taxon(run_dir, genome_ids_a, genome_ids_b, sico_files):
    """Separate multiple sequence alignments with sequences from two taxa out into separate files per taxon."""
    #Collections to hold split files
    taxon_a_files = []
    taxon_b_files = []
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