<commit_before># ----------------------------------------------------------------------------
# Copyright (c) 2015--, The WGS-HGT Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------

"""
Reformat input files to format accepted by given HGT tool
=========================================================
"""

import click

from os import remove
from os.path import join
from skbio import TreeNode, TabularMSA, Sequence, Protein, DNA
from collections import OrderedDict


def join_trees(gene_tree,
               species_tree,
               output_tree_fp):
    """ Concatenate Newick trees into one file (species followed by gene).

    Parameters
    ----------
    gene_tree: skbio.TreeNode<commit_msg>removed an unused module from reformat_input.py<commit_after># ----------------------------------------------------------------------------
# Copyright (c) 2015--, The WGS-HGT Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------

"""
Reformat input files to format accepted by given HGT tool
=========================================================
"""

import click

from os.path import join
from skbio import TreeNode, TabularMSA, Sequence, Protein, DNA
from collections import OrderedDict


def join_trees(gene_tree,
               species_tree,
               output_tree_fp):
    """ Concatenate Newick trees into one file (species followed by gene).

    Parameters
    ----------
    gene_tree: skbio.TreeNode
{'fraction_non_alphanumeric': 0.2948717948717949, 'fraction_numerical': 0.004459308807134894, 'mean_word_length': 1.8446909667194928, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1177950', 'n_tokens_mistral': 418, 'n_tokens_neox': 386, 'n_words': 156}