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import unittest
import os
import filecmp
from pymummer import nucmer
modules_dir = os.path.dirname(os.path.abspath(nucmer.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')
class TestRunner(unittest.TestCase):
def test_nucmer_command(self):
'''test _nucmer_command'''
tests = [
[nucmer.Runner('ref', 'qry', 'outfile'), 'nucmer -p pre ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', breaklen=42), 'nucmer -p pre -b 42 ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11), 'nucmer -p pre -D 11 ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11, promer=True), 'promer -p pre ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', maxmatch=True), 'nucmer -p pre --maxmatch ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', mincluster=42), 'nucmer -p pre -c 42 ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', simplify=False), 'nucmer -p pre --nosimplify ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', promer=True), 'promer -p pre ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', promer=True, breaklen=42), 'promer -p pre -b 42 ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', promer=True, maxmatch=True), 'promer -p pre --maxmatch ref qry'],
[nucmer.Runner('ref', 'qry', 'outfile', promer=True, simplify=False), 'promer -p pre ref qry']
]
for l in tests:
self.assertEqual(l[0]._nucmer_command('ref', 'qry', 'pre'), l[1])
def test_delta_filter_command(self):
'''test _delta_filter_command'''
tests = [
[nucmer.Runner('ref', 'qry', 'outfile'), 'delta-filter infile > outfile'],
[nucmer.Runner('ref', 'qry', 'outfile', min_id=42), 'delta-filter -i 42 infile > outfile'],
[nucmer.Runner('ref', 'qry', 'outfile', min_length=43), 'delta-filter -l 43 infile > outfile'],
]
for l in tests:
self.assertEqual(l[0]._delta_filter_command('infile', 'outfile'), l[1])
def test_show_coords_command(self):
'''test _show_coords_command'''
tests = [
[nucmer.Runner('ref', 'qry', 'outfile', coords_header=False), 'show-coords -dTlro -H infile > outfile'],
[nucmer.Runner('ref', 'qry', 'outfile'), 'show-coords -dTlro infile > outfile']
]
for l in tests:
self.assertEqual(l[0]._show_coords_command('infile', 'outfile'), l[1])
def test_show_snps_command(self):
'''test _show_snps_command'''
tests = [
[nucmer.Runner('ref', 'qry', 'outfile', snps_header=False), 'show-snps -TClr -H infile > outfile'],
[nucmer.Runner('ref', 'qry', 'outfile'), 'show-snps -TClr infile > outfile'],
[nucmer.Runner('ref', 'qry', 'outfile', show_snps_C=False), 'show-snps -Tlr infile > outfile']
]
for nuc_obj, expected in tests:
self.assertEqual(nuc_obj._show_snps_command('infile', 'outfile'), expected)
def test_write_script_no_snps(self):
'''test _write_script no snps'''
tmp_script = 'tmp.script.sh'
r = nucmer.Runner('ref', 'qry', 'outfile')
r._write_script(tmp_script, 'ref', 'qry', 'outfile')
expected = os.path.join(data_dir, 'nucmer_test_write_script_no_snps.sh')
self.assertTrue(filecmp.cmp(expected, tmp_script, shallow=False))
os.unlink(tmp_script)
def test_write_script_with_snps(self):
'''test _write_script with snps'''
tmp_script = 'tmp.script.sh'
r = nucmer.Runner('ref', 'qry', 'outfile', show_snps='outfile.snps')
r._write_script(tmp_script, 'ref', 'qry', 'outfile')
expected = os.path.join(data_dir, 'nucmer_test_write_script_with_snps.sh')
self.assertTrue(filecmp.cmp(expected, tmp_script, shallow=False))
os.unlink(tmp_script)
def test_run_nucmer(self):
'''test run_nucmer'''
qry = os.path.join(data_dir, 'nucmer_test_qry.fa')
ref = os.path.join(data_dir, 'nucmer_test_ref.fa')
tmp_out = 'tmp.nucmer.out'
runner = nucmer.Runner(ref, qry, tmp_out, coords_header=False, show_snps=True, snps_header=False)
runner.run()
expected = os.path.join(data_dir, 'nucmer_test_out.coords')
self.assertTrue(filecmp.cmp(tmp_out, expected, shallow=False))
self.assertTrue(filecmp.cmp(tmp_out + '.snps', expected + '.snps', shallow=False))
os.unlink(tmp_out)
os.unlink(tmp_out + '.snps')
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