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import unittest
import os
import filecmp
from pymummer import coords_file, alignment
data_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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