# Copyright 2009 by David Winter.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Tests for EmbossPhylipNew module."""

import os
import sys
import unittest
import warnings

from Bio import AlignIO
from Bio import BiopythonDeprecationWarning
from Bio import MissingExternalDependencyError
from Bio.Nexus import Trees  # One day we should use planned TreeIO module

with warnings.catch_warnings():
    warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
    from Bio.Emboss.Applications import FConsenseCommandline
    from Bio.Emboss.Applications import FDNADistCommandline
    from Bio.Emboss.Applications import FDNAParsCommandline
    from Bio.Emboss.Applications import FNeighborCommandline
    from Bio.Emboss.Applications import FProtDistCommandline
    from Bio.Emboss.Applications import FProtParsCommandline
    from Bio.Emboss.Applications import FSeqBootCommandline
    from Bio.Emboss.Applications import FTreeDistCommandline

# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"

exes_wanted = [
    "fdnadist",
    "fneighbor",
    "fprotdist",
    "fprotpars",
    "fconsense",
    "fseqboot",
    "ftreedist",
    "fdnapars",
]
exes = {}  # Dictionary mapping from names to exe locations

if "EMBOSS_ROOT" in os.environ:
    # Windows default installation path is C:\mEMBOSS which contains the exes.
    # EMBOSS also sets an environment variable which we will check for.
    path = os.environ["EMBOSS_ROOT"]
    if os.path.isdir(path):
        for name in exes_wanted:
            if os.path.isfile(os.path.join(path, name + ".exe")):
                exes[name] = os.path.join(path, name + ".exe")
    del path, name
if sys.platform != "win32":
    from subprocess import getoutput

    for name in exes_wanted:
        # This will "just work" if installed on the path as normal on Unix
        output = getoutput(f"{name} -help")
        if "not found" not in output and "not recognized" not in output:
            exes[name] = name
        del output
    del name

if len(exes) < len(exes_wanted):
    raise MissingExternalDependencyError(
        "Install the Emboss package 'PhylipNew' if you want to use the "
        "Bio.Emboss.Applications wrappers for phylogenetic tools."
    )

# #########################################################################


# A few top level functions that are called repeatedly in the test cases
def clean_up():
    """Delete tests files (to be used as tearDown() function in test fixtures)."""
    for filename in ["test_file", "Phylip/opuntia.phy", "Phylip/hedgehog.phy"]:
        if os.path.isfile(filename):
            os.remove(filename)


def parse_trees(filename):
    """Parse trees.

    Helper function until we have Bio.Phylo on trunk.
    """
    # TODO - Can this be removed now?
    with open("test_file") as handle:
        data = handle.read()
    for tree_str in data.split(";\n"):
        if tree_str:
            yield Trees.Tree(tree_str + ";")


class DistanceTests(unittest.TestCase):
    """Tests for calculating distance based phylogenetic trees with phylip."""

    def tearDown(self):
        clean_up()

    test_taxa = [
        "Archaeohip",
        "Calippus",
        "Hypohippus",
        "M._secundu",
        "Merychippu",
        "Mesohippus",
        "Nannipus",
        "Neohippari",
        "Parahippus",
        "Pliohippus",
    ]

    def distances_from_alignment(self, filename, DNA=True):
        """Check we can make a distance matrix from a given alignment."""
        self.assertTrue(os.path.isfile(filename), f"Missing {filename}")
        if DNA:
            cline = FDNADistCommandline(
                exes["fdnadist"],
                method="j",
                sequence=filename,
                outfile="test_file",
                auto=True,
            )
        else:
            cline = FProtDistCommandline(
                exes["fprotdist"],
                method="j",
                sequence=filename,
                outfile="test_file",
                auto=True,
            )
        stdout, strerr = cline()
        # biopython can't grok distance matrices, so we'll just check it exists
        self.assertTrue(os.path.isfile("test_file"))

    def tree_from_distances(self, filename):
        """Check we can estimate a tree from a distance matrix."""
        self.assertTrue(os.path.isfile(filename), f"Missing {filename}")
        cline = FNeighborCommandline(
            exes["fneighbor"],
            datafile=filename,
            outtreefile="test_file",
            auto=True,
            filter=True,
        )
        stdout, stderr = cline()
        for tree in parse_trees("test_file"):
            tree_taxa = [t.replace(" ", "_") for t in tree.get_taxa()]
            self.assertEqual(self.test_taxa, sorted(tree_taxa))

    def test_distances_from_phylip_DNA(self):
        """Calculate a distance matrix from an phylip alignment."""
        self.distances_from_alignment("Phylip/horses.phy")

    def test_distances_from_AlignIO_DNA(self):
        """Calculate a distance matrix from an alignment written by AlignIO."""
        n = AlignIO.convert(
            "Clustalw/opuntia.aln", "clustal", "Phylip/opuntia.phy", "phylip"
        )
        self.assertEqual(n, 1)
        self.distances_from_alignment("Phylip/opuntia.phy")

    # def test_distances_from_bootstrapped_phylip_DNA(self):
    #    """Calculate a set of distance matrices from phylip alignments"""
    #    self.distances_from_alignment("Phylip/bs_horses.phy")

    # fprotdist tests
    def test_distances_from_protein_phylip(self):
        """Calculate a distance matrix from phylip protein alignment."""
        self.distances_from_alignment("Phylip/interlaced.phy", DNA=False)

    def test_distances_from_protein_AlignIO(self):
        """Calculate distance matrix from an AlignIO written protein alignment."""
        n = AlignIO.convert(
            "Clustalw/hedgehog.aln", "clustal", "Phylip/hedgehog.phy", "phylip"
        )
        self.assertEqual(n, 1)
        self.distances_from_alignment("Phylip/hedgehog.phy", DNA=False)

    # def test_distances_from_bootstrapped_phylip_protein(self):
    #    """Calculate distance matrices from a bootstrapped protein alignment"""
    #    self.distances_from_alignment("Clustalw/bs_interlaced.phy", DNA=False)

    # fneighbor tests
    # def test_tree_from_distances(self):
    #    """Estimate tree from distance matrix and parse it."""
    #    self.tree_from_distances("Phylip/horses.fdnadist")

    # This one won't work because of a bug in EMBOSS 6.0.1
    # def test_tree_from_bootstrapped_distances(self):
    #    """Estimate tree from bootstrapped distance matrix and parse it"""
    #    self.tree_from_distances("Phylip/bs_horses.fdnadist")


class ParsimonyTests(unittest.TestCase):
    """Tests for estimating parsimony based phylogenetic trees with phylip."""

    def tearDown(self):
        clean_up()

    def parsimony_tree(self, filename, format, DNA=True):
        """Estimate a parsimony tree from an alignment."""
        self.assertTrue(os.path.isfile(filename), f"Missing {filename}")
        if DNA:
            cline = FDNAParsCommandline(
                exes["fdnapars"],
                sequence=filename,
                outtreefile="test_file",
                auto=True,
                stdout=True,
            )
        else:
            cline = FProtParsCommandline(
                exes["fprotpars"],
                sequence=filename,
                outtreefile="test_file",
                auto=True,
                stdout=True,
            )
        stdout, stderr = cline()
        with open(filename) as handle:
            a_taxa = [
                s.name.replace(" ", "_") for s in next(AlignIO.parse(handle, format))
            ]
        for tree in parse_trees("test_file"):
            t_taxa = [t.replace(" ", "_") for t in tree.get_taxa()]
            self.assertEqual(sorted(a_taxa), sorted(t_taxa))

    # fdnapars tests
    # def test_parsimony_tree_from_phylip_DNA(self):
    #    """Make a parsimony tree from a phylip DNA alignment"""
    #    self.parsimony_tree("Phylip/horses.phy", "phylip")

    def test_parsimony_tree_from_AlignIO_DNA(self):
        """Make a parsimony tree from an alignment written with AlignIO."""
        n = AlignIO.convert(
            "Clustalw/opuntia.aln", "clustal", "Phylip/opuntia.phy", "phylip"
        )
        self.assertEqual(n, 1)
        self.parsimony_tree("Phylip/opuntia.phy", "phylip")

    # def test_parsimony_bootstrapped_phylip_DNA(self):
    #    """Make a parsimony tree from a bootstrapped phylip DNA alignment"""
    #    self.parsimony_tree("Phylip/bs_horses.phy", "phylip")

    # fprotpars tests
    # def test_parsimony_tree_from_phylip_protein(self):
    #    """Make a parsimony tree from a phylip DNA alignment"""
    #    self.parsimony_tree("Phylip/interlaced.phy", "phylip", DNA=False)

    def test_parsimony_from_AlignIO_protein(self):
        """Make a parsimony tree from protein alignment written with AlignIO."""
        n = AlignIO.convert(
            "Clustalw/hedgehog.aln", "clustal", "Phylip/hedgehog.phy", "phylip"
        )
        self.parsimony_tree("Phylip/interlaced.phy", "phylip", DNA=False)

    # def test_parsimony_tree_bootstrapped_phylip_protein(self):
    #    """Make a parsimony tree from a phylip DNA alignment"""
    #    self.parsimony_tree("Phylip/bs_interlaced.phy", "phylip", DNA=False)


class BootstrapTests(unittest.TestCase):
    """Tests for pseudosampling alignments with fseqboot."""

    def tearDown(self):
        clean_up()

    def check_bootstrap(self, filename, format, align_type="d"):
        """Check we can use fseqboot to pseudosample an alignment.

        The align_type type argument is passed to the commandline object to
        set the output format to use (from [D]na,[p]rotein and [r]na )
        """
        self.assertTrue(os.path.isfile(filename), f"Missing {filename}")
        cline = FSeqBootCommandline(
            exes["fseqboot"],
            sequence=filename,
            outfile="test_file",
            seqtype=align_type,
            reps=2,
            auto=True,
            filter=True,
        )
        stdout, stderr = cline()
        # the resultant file should have 2 alignments...
        with open("test_file") as handle:
            bs = list(AlignIO.parse(handle, format))
        self.assertEqual(len(bs), 2)
        # ..and each name in the original alignment...
        with open(filename) as handle:
            a_names = [s.name.replace(" ", "_") for s in AlignIO.read(handle, format)]
        # ...should be in each alignment in the bootstrapped file
        for a in bs:
            self.assertEqual(a_names, [s.name.replace(" ", "_") for s in a])

    def test_bootstrap_phylip_DNA(self):
        """Pseudosample a phylip DNA alignment."""
        self.check_bootstrap("Phylip/horses.phy", "phylip")

    def test_bootstrap_AlignIO_DNA(self):
        """Pseudosample a phylip DNA alignment written with AlignIO."""
        n = AlignIO.convert(
            "Clustalw/opuntia.aln", "clustal", "Phylip/opuntia.phy", "phylip"
        )
        self.assertEqual(n, 1)
        self.check_bootstrap("Phylip/opuntia.phy", "phylip")

    def test_bootstrap_phylip_protein(self):
        """Pseudosample a phylip protein alignment."""
        self.check_bootstrap("Phylip/interlaced.phy", "phylip", "p")

    def test_bootstrap_AlignIO_protein(self):
        """Pseudosample a phylip protein alignment written with AlignIO."""
        n = AlignIO.convert(
            "Clustalw/hedgehog.aln", "clustal", "Phylip/hedgehog.phy", "phylip"
        )
        self.check_bootstrap("Phylip/hedgehog.phy", "phylip", "p")


class TreeComparisonTests(unittest.TestCase):
    """Tests for comparing phylogenetic trees with phylip tools."""

    def tearDown(self):
        clean_up()

    def test_fconsense(self):
        """Calculate a consensus tree with fconsense."""
        cline = FConsenseCommandline(
            exes["fconsense"],
            intreefile="Phylip/horses.tree",
            outtreefile="test_file",
            auto=True,
            filter=True,
        )
        stdout, stderr = cline()
        # Split the next and get_taxa into two steps to help 2to3 work
        tree1 = next(parse_trees("test_file"))
        taxa1 = tree1.get_taxa()
        for tree in parse_trees("Phylip/horses.tree"):
            taxa2 = tree.get_taxa()
            self.assertEqual(sorted(taxa1), sorted(taxa2))

    def test_ftreedist(self):
        """Calculate the distance between trees with ftreedist."""
        cline = FTreeDistCommandline(
            exes["ftreedist"],
            intreefile="Phylip/horses.tree",
            outfile="test_file",
            auto=True,
            filter=True,
        )
        stdout, stderr = cline()
        self.assertTrue(os.path.isfile("test_file"))


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
    clean_up()
