# Copyright 2013 by Saket Choudhary.  Based on test_Clustalw_tool.py by Peter
# Cock .
#
# 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.

from Bio import MissingExternalDependencyError
import sys
import os
import unittest
# TODO from Bio.Sequencing.Applications import BwaBwaswCommandline
from Bio.Sequencing.Applications import BwaIndexCommandline
from Bio.Sequencing.Applications import BwaAlignCommandline
from Bio.Sequencing.Applications import BwaSamseCommandline
from Bio.Sequencing.Applications import BwaSampeCommandline


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

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

bwa_exe = None
if sys.platform == "win32":
    # TODO - Check the path?
    try:
        # This can vary depending on the Windows language.
        prog_files = os.environ["PROGRAMFILES"]
    except KeyError:
        prog_files = r"C:\Program Files"
    likely_dirs = ["bwa", "bwa-0.6.2", ""]
    likely_exes = ["bwa"]
    for folder in likely_dirs:
        if os.path.isdir(os.path.join(prog_files, folder)):
            for filename in likely_exes:
                if os.path.isfile(os.path.join(prog_files, folder, filename)):
                    bwa_exe = os.path.join(prog_files, folder, filename)
                    break
            if bwa_exe:
                break
else:
    from Bio._py3k import getoutput
    output = getoutput("bwa")

    # Since "not found" may be in another language, try and be sure this is
    # really the bwa tool's output
    bwa_found = False
    if "not found" not in output and "bwa" in output \
            and "alignment via Burrows-Wheeler transformation" in output:
        bwa_exe = "bwa"
    skip_aln_tests = False
    aln_output = getoutput("bwa aln")
    if "unrecognized" in aln_output:
        skip_aln_tests = True
        print("'bwa aln' is unrecognized, skipping aln/samse/sampe tests")

if not bwa_exe:
    raise MissingExternalDependencyError("Install bwa and correctly set"
                                         " the file path to the program if"
                                         " you want to use it from Biopython")


class BwaTestCase(unittest.TestCase):
    """Class for implementing BWA test cases"""
    def setUp(self):
        self.reference_file = "BWA/human_g1k_v37_truncated.fasta"
        self.reference_extensions = ['amb', 'ann', 'bwt', 'pac', 'sa']
        self.infile1 = "BWA/HNSCC1_1_truncated.fastq"
        self.infile2 = "BWA/HNSCC1_2_truncated.fastq"
        self.saifile1 = "BWA/1.sai"
        self.saifile2 = "BWA/2.sai"
        self.samfile1 = "BWA/1.sam"
        self.samfile2 = "BWA/2.sam"
        self.samfile = "BWA/out.sam"
        self.files_to_clean = [self.saifile1, self.saifile2,
                               self.samfile1, self.samfile2,
                               self.samfile]

    def tearDown(self):
        for filename in self.files_to_clean:
            if os.path.isfile(filename):
                os.remove(filename)
        for extension in self.reference_extensions:
            index_file = self.reference_file + "." + extension
            if os.path.exists(index_file):
                os.remove(index_file)

    def test_index(self):
        """Test for creating index files for the reference genome fasta file"""
        cmdline = BwaIndexCommandline(bwa_exe)
        cmdline.set_parameter("infile", self.reference_file)
        cmdline.set_parameter("algorithm", "bwtsw")
        stdout, stderr = cmdline()
        for extension in self.reference_extensions:
            index_file = self.reference_file + "." + extension
            self.assertTrue(os.path.exists(index_file),
                            "Index File %s not found"
                            % (index_file))
        self.assertTrue(stdout.startswith("[bwt_gen]"),
                        "FASTA indexing failed:\n%s\nStdout:%s"
                        % (cmdline, stdout))

    def do_aln(self, in_file, out_file):
        """Test for generating sai files given the reference and read file"""
        cmdline = BwaAlignCommandline(bwa_exe)
        cmdline.set_parameter("reference", self.reference_file)
        cmdline.read_file = in_file
        self.assertTrue(os.path.isfile(in_file))
        stdout, stderr = cmdline(stdout=out_file)

        self.assertTrue("fail to locate the index" not in stderr,
                        "Error aligning sequence to reference:\n%s\nStderr:%s"
                        % (cmdline, stderr))

    def create_fasta_index(self):
        """Creates index for fasta file.

        BWA requires an indexed fasta for each alignment operation.
        This should be called to create an index before any alignment
        operation.
        """
        cmdline = BwaIndexCommandline(bwa_exe)
        cmdline.set_parameter("infile", self.reference_file)
        cmdline.set_parameter("algorithm", "bwtsw")
        stdout, stderr = cmdline()

    if not skip_aln_tests:

        def test_samse(self):
            """Test for single end sequencing """
            self.create_fasta_index()
            self.do_aln(self.infile1, self.saifile1)
            cmdline = BwaSamseCommandline(bwa_exe)
            cmdline.set_parameter("reference", self.reference_file)
            cmdline.set_parameter("read_file", self.infile1)
            cmdline.set_parameter("sai_file", self.saifile1)
            stdout, stderr = cmdline(stdout=self.samfile1)

            with open(self.samfile1, "r") as handle:
                headline = handle.readline()
            self.assertTrue(headline.startswith("@SQ"),
                            "Error generating sam files:\n%s\nOutput starts:%s"
                            % (cmdline, headline))

        def test_sampe(self):
            """Test for generating samfile by paired end sequencing"""
            self.create_fasta_index()

            # Generate sai files from paired end data
            self.do_aln(self.infile1, self.saifile1)
            self.do_aln(self.infile2, self.saifile2)

            cmdline = BwaSampeCommandline(bwa_exe)
            cmdline.set_parameter("reference", self.reference_file)
            cmdline.set_parameter("sai_file1", self.saifile1)
            cmdline.set_parameter("sai_file2", self.saifile2)
            cmdline.set_parameter("read_file1", self.infile1)
            cmdline.set_parameter("read_file2", self.infile2)
            stdout, stderr = cmdline(stdout=self.samfile)

            with open(self.samfile, "r") as handle:
                headline = handle.readline()
            self.assertTrue(headline.startswith("@SQ"),
                            "Error generating sam files:\n%s\nOutput starts:%s"
                            % (cmdline, headline))


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