BjornFJohansson/pydna

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license.  Please see the LICENSE.txt file that should have been included
# as part of this package.
"""docstring."""
from operator import add
from functools import reduce
import networkx as _nx
from itertools import permutations
import logging as _logging

_module_logger = _logging.getLogger("pydna." + __name__)


def ligate(fragments: list):
    """docstring."""
    G = _nx.DiGraph()
    G.add_nodes_from(["begin", "end"])
    fragments = fragments[:]

    fragments.extend(f.rc() for f in fragments[1:])

    for node in fragments:
        G.add_edge("begin", node)
        G.add_edge(node, "end")

    for seq1, seq2 in permutations(fragments, 2):
        try:
            seq1 + seq2
        except TypeError as err:
            if str(err) != "sticky ends not compatible!":
                raise
        else:
            if seq1.seq.three_prime_end() != (
                "blunt",
                "",
            ) and seq2.seq.five_prime_end() != ("blunt", ""):
                G.add_edge(seq1, seq2)
                try:
                    G.remove_edge("begin", seq2)
                except _nx.NetworkXError as err:
                    if "not in graph" not in str(err):
                        raise
                try:
                    G.remove_edge(seq1, "end")
                except _nx.NetworkXError as err:
                    if "not in graph" not in str(err):
                        raise

    cpaths = [p for p in sorted(_nx.simple_cycles(G), key=len) if len(p) > 1]
    csequences = [reduce(add, x).looped() for x in cpaths]
    lpaths = [p for p in sorted(_nx.all_simple_paths(G, "begin", "end"), key=len) if len(p) > 3]
    lsequences = [reduce(add, lp[1:-1]) for lp in lpaths]

    return csequences, lsequences


if __name__ == "__main__":
    import os as _os

    cached = _os.getenv("pydna_cached_funcs", "")
    _os.environ["pydna_cached_funcs"] = ""
    import doctest

    doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
    _os.environ["pydna_cached_funcs"] = cached