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import unittest
import os
import filecmp
from pymummer import coords_file, alignment
modules_dir = os.path.dirname(os.path.abspath(coords_file.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')
class TestCoordsFile(unittest.TestCase):
def test_coords_file(self):
'''test coords_file'''
expected = [
'\t'.join(['61', '900', '1', '840', '840', '840', '99.76', '1000', '840', '1', '1', 'test_ref1', 'test_qry1', '[CONTAINS]']),
'\t'.join(['62', '901', '2', '841', '841', '850', '99.66', '999', '839', '1', '1', 'test_ref2', 'test_qry2', '[CONTAINS]']),
'\t'.join(['63', '902', '3', '842', '842', '860', '99.56', '998', '838', '1', '1', 'test_ref3', 'test_qry3', '[CONTAINS]'])
]
expected = [alignment.Alignment(x) for x in expected]
infiles = [os.path.join(data_dir, 'coords_file_test_with_header.coords'), os.path.join(data_dir, 'coords_file_test_no_header.coords')]
for fname in infiles:
fr = coords_file.reader(fname)
alignments = [x for x in fr]
self.assertEqual(alignments, expected)
def test_convert_to_msp_crunch_no_offset(self):
'''Test convert_to_msp_crunch with no offsets'''
infile = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.coords')
expected = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.no_offset.crunch')
tmpfile = 'tmp.test_convert_to_msp_crunch_no_offset.crunch'
coords_file.convert_to_msp_crunch(infile, tmpfile)
self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False))
os.unlink(tmpfile)
def test_convert_to_msp_crunch_with_offset(self):
'''Test convert_to_msp_crunch with offsets'''
infile = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.coords')
ref_fai = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.ref.fa.fai')
qry_fai = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.qry.fa.fai')
expected = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.with_offset.crunch')
tmpfile = 'tmp.test_convert_to_msp_crunch_with_offset.crunch'
with self.assertRaises(coords_file.Error):
coords_file.convert_to_msp_crunch(infile, tmpfile, ref_fai=ref_fai)
coords_file.convert_to_msp_crunch(infile, tmpfile, qry_fai=qry_fai)
coords_file.convert_to_msp_crunch(infile, tmpfile, ref_fai=ref_fai, qry_fai=qry_fai)
self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False))
os.unlink(tmpfile)
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