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import unittest
import os
from pymummer import snp_file, snp, variant
modules_dir = os.path.dirname(os.path.abspath(snp_file.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')
class TestUtils(unittest.TestCase):
def test_snp_file(self):
'''test coords_file'''
expected = [
'\t'.join(['133', 'G', '.', '122', '1', '122', '500', '489', '1', '1', 'ref', 'qry']),
'\t'.join(['143', '.', 'C', '131', '1', '132', '500', '489', '1', '1', 'ref', 'qry']),
'\t'.join(['253', 'T', 'A', '242', '120', '242', '500', '489', '1', '1', 'ref', 'qry'])
]
expected = [snp.Snp(x) for x in expected]
infiles = [os.path.join(data_dir, 'snp_file_test_with_header.snps'), os.path.join(data_dir, 'snp_file_test_no_header.snps')]
for fname in infiles:
fr = snp_file.reader(fname)
snps = [x for x in fr]
self.assertEqual(snps, expected)
def test_get_all_variants(self):
'''Test load all variants from file'''
deletion_snps = [
'\t'.join(['125', 'T', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']),
'\t'.join(['126', 'A', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']),
'\t'.join(['127', 'C', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']),
]
deletion_snps = [snp.Snp(x) for x in deletion_snps]
deletion_variant = variant.Variant(deletion_snps[0])
deletion_variant.update_indel(deletion_snps[1])
deletion_variant.update_indel(deletion_snps[2])
just_a_snp = '\t'.join(['386', 'C', 'T', '383', '115', '115', '500', '497', '1', '1', 'ref1', 'qry1'])
snp_variant = variant.Variant(snp.Snp(just_a_snp))
insertion_snps = [
'\t'.join(['479', '.', 'G', '480', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']),
'\t'.join(['479', '.', 'A', '481', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']),
'\t'.join(['479', '.', 'T', '482', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']),
'\t'.join(['479', '.', 'A', '483', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']),
]
insertion_snps = [snp.Snp(x) for x in insertion_snps]
insertion_variant = variant.Variant(insertion_snps[0])
for i in range(1, len(insertion_snps)):
insertion_variant.update_indel(insertion_snps[i])
variants_from_file = snp_file.get_all_variants(os.path.join(data_dir, 'snp_file_test_get_all_variants.snps'))
self.assertEqual(len(variants_from_file), 3)
self.assertEqual(variants_from_file[0], deletion_variant)
self.assertEqual(variants_from_file[1], snp_variant)
self.assertEqual(variants_from_file[2], insertion_variant)
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