import unittest
import copy
import os
from pymummer import variant, snp

modules_dir = os.path.dirname(os.path.abspath(variant.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')


class TestVariant(unittest.TestCase):
    def test_init(self):
        '''Test init gets correct variant type'''
        lines = [
            ['42', 'T', 'A', '42', '42', '42', '1000', '1000', '1', '1', 'ref', 'ref'],
            ['242', 'G', '.', '241', '1', '241', '1000', '1000', '1', '1', 'ref', 'ref'],
            ['300', '.', 'G', '298', '0', '298', '1000', '1000', '1', '1', 'ref', 'ref']
        ]

        variants = [variant.Variant(snp.Snp('\t'.join(x))) for x in lines]
        expected = [variant.SNP, variant.DEL, variant.INS]
        for i in range(len(lines)):
            self.assertEqual(variants[i].var_type, expected[i])


    def test_update_indel_no_change(self):
        '''Test update_indel does nothing in the right cases'''
        initial_vars = [
            snp.Snp('\t'.join(['42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
        ]

        to_add = [
            snp.Snp('\t'.join(['142', 'A', '.', '1000', 'x', 'x', '2000', '3000', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['142', '.', 'A', '1000', 'x', 'x', '2000', '3000', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref2', 'qry'])),
            snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry2'])),
            snp.Snp('\t'.join(['44', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref2', 'qry'])),
            snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry2'])),
            snp.Snp('\t'.join(['44', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
            snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
        ]

        assert len(initial_vars) == len(to_add)

        for i in range(len(initial_vars)):
            var = variant.Variant(initial_vars[i])
            var_original = copy.copy(var)
            self.assertFalse(var.update_indel(to_add[i]))
            self.assertEqual(var, var_original)

    def test_update_indel_insertion(self):
        '''Test update_indel extends insertions correctly'''
        insertion = variant.Variant(snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '-1', 'ref', 'qry'])))
        to_add = snp.Snp('\t'.join(['42', '.', 'C', '101', 'x', 'x', '300', '400', 'x', '-1', 'ref', 'qry']))
        expected = copy.copy(insertion)
        # coords stored zero-based, so subtract 1 from the real expected coords
        expected.ref_start = 41
        expected.ref_end = 41
        expected.ref_length = 300
        expected.ref_name = 'ref'
        expected.ref_base = '.'
        expected.qry_start = 99
        expected.qry_end = 100
        expected.qry_length = 400
        expected.qry_name = 'qry'
        expected.qry_base = 'AC'
        self.assertTrue(insertion.update_indel(to_add))
        self.assertEqual(expected, insertion)


    def test_update_indel_deletion(self):
        '''Test update_indel extends deletions correctly'''
        deletion = variant.Variant(snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])))
        to_add = snp.Snp('\t'.join(['43', 'C', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry']))
        expected = copy.copy(deletion)
        # coords stored zero-based, so subtract 1 from the real expected coords
        expected.ref_start = 41
        expected.ref_end = 42
        expected.ref_length = 300
        expected.ref_name = 'ref'
        expected.ref_base = 'AC'
        expected.qry_start = 99
        expected.qry_end = 99
        expected.qry_length = 400
        expected.qry_name = 'qry'
        expected.qry_base = '.'
        self.assertTrue(deletion.update_indel(to_add))
        self.assertEqual(expected, deletion)