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import unittest
import os
import filecmp
from pymummer import nucmer
data_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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