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"""Tests for SeqIO TwoBitIO module."""
import unittest
from Bio import SeqIO
from Bio.Seq import MutableSeq
from Bio.Seq import Seq
from Bio.Seq import UndefinedSequenceError
from Bio.SeqRecord import SeqRecord
class Parsing(unittest.TestCase):
"""Test parsing 2bit files."""
def setUp(self):
path = "TwoBit/sequence.fa"
records = SeqIO.parse(path, "fasta")
self.records = list(records)
def test_littleendian(self, step=5):
path = "TwoBit/sequence.littleendian.2bit"
with open(path, "rb") as stream:
records = SeqIO.parse(stream, "twobit")
self.assertEqual(records.byteorder, "little")
self.assertEqual(len(self.records), len(records))
for record1, record2 in zip(self.records, records):
self.assertEqual(record1.id, record2.id)
seq1 = record1.seq
seq2 = record2.seq
self.assertEqual(seq1, seq2)
n = len(seq1)
for i in range(0, n, step):
for j in range(i, n, step):
self.assertEqual(seq1[i:j], seq2[i:j])
self.assertEqual(repr(seq1[i:j]), repr(seq2[i:j]))
def test_bigendian(self, step=5):
path = "TwoBit/sequence.bigendian.2bit"
with open(path, "rb") as stream:
records = SeqIO.parse(stream, "twobit")
self.assertEqual(len(records), 6)
self.assertEqual(records.byteorder, "big")
for record1, record2 in zip(self.records, records):
self.assertEqual(record1.id, record2.id)
seq1 = record1.seq
seq2 = record2.seq
self.assertEqual(seq1, seq2)
n = len(seq1)
for i in range(0, n, step):
for j in range(i, n, step):
self.assertEqual(seq1[i:j], seq2[i:j])
self.assertEqual(repr(seq1[i:j]), repr(seq2[i:j]))
def test_sequence_long(self):
path = "TwoBit/sequence.long.2bit"
with open(path, "rb") as stream:
with self.assertRaises(ValueError) as cm:
SeqIO.parse(stream, "twobit")
self.assertEqual(
str(cm.exception),
"version-1 twoBit files with 64-bit offsets for index are currently not supported",
)
class TestComparisons(unittest.TestCase):
"""Test comparisons of sequences read from 2bit files to Seq and other objects."""
def setUp(self):
path = "TwoBit/sequence.bigendian.2bit"
self.stream = open(path, "rb")
records = SeqIO.parse(self.stream, "twobit")
record1 = next(records)
record2 = next(records)
self.seq1a = record1.seq
self.seq2a = record2.seq
path = "TwoBit/sequence.fa"
records = SeqIO.parse(path, "fasta")
record1 = next(records)
record2 = next(records)
self.seq1b = record1.seq
self.seq2b = record2.seq
def tearDown(self):
self.stream.close()
def test_eq(self):
seq1a = self.seq1a
seq2a = self.seq2a
seq1b = self.seq1b
seq2b = self.seq2b
self.assertEqual(seq1a, seq1b)
self.assertEqual(seq2a, seq2b)
self.assertEqual(seq1a, seq1a)
self.assertEqual(seq2a, seq2a)
with self.assertRaises(UndefinedSequenceError):
seq1a == Seq(None, len(seq1a))
with self.assertRaises(UndefinedSequenceError):
seq2a == Seq(None, len(seq2a))
with self.assertRaises(UndefinedSequenceError):
seq1a == Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2a == Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq1a)) == seq1a
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq2a)) == seq2a
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) == seq1a
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) == seq2a
def test_ne(self):
seq1a = self.seq1a
seq2a = self.seq2a
seq1b = self.seq1b
seq2b = self.seq2b
self.assertNotEqual(seq1a, seq2a)
self.assertNotEqual(seq1a, seq2b)
with self.assertRaises(UndefinedSequenceError):
seq1a != Seq(None, len(seq1a))
with self.assertRaises(UndefinedSequenceError):
seq2a != Seq(None, len(seq2a))
with self.assertRaises(UndefinedSequenceError):
seq1a != Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2a != Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq1a)) != seq1a
with self.assertRaises(UndefinedSequenceError):
Seq(None, len(seq2a)) != seq2a
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) != seq1a
with self.assertRaises(UndefinedSequenceError):
Seq(None, 10) != seq2a
def test_lt(self):
seq1 = self.seq1a
seq2 = self.seq2a
self.assertLess(seq1, seq2)
self.assertLess("AA", seq1)
self.assertLess(seq1, "TT")
self.assertLess("AA", seq2)
self.assertLess(seq2, "TTT")
self.assertLess(b"AA", seq1)
self.assertLess(seq1, b"TT")
self.assertLess(b"AA", seq2)
self.assertLess(seq2, b"TTT")
self.assertLess(Seq("AA"), seq1)
self.assertLess(seq1, Seq("TT"))
self.assertLess(Seq("AA"), seq2)
self.assertLess(seq2, Seq("TTT"))
self.assertLess(MutableSeq("AA"), seq1)
self.assertLess(seq1, MutableSeq("TT"))
self.assertLess(MutableSeq("AA"), seq2)
self.assertLess(seq2, MutableSeq("TTT"))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 < Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 < Seq(None, 10)
def test_le(self):
seq1 = self.seq1a
seq2 = self.seq2a
self.assertLessEqual(seq1, seq2)
self.assertLessEqual(seq1, "TT")
self.assertLessEqual("TT", seq2)
self.assertLessEqual(seq1, b"TT")
self.assertLessEqual("TT", seq2)
self.assertLessEqual(seq1, Seq("TT"))
self.assertLessEqual("TT", seq2)
self.assertLessEqual(seq1, MutableSeq("TT"))
self.assertLessEqual(MutableSeq("TT"), seq2)
self.assertLessEqual("AA", seq1)
self.assertLessEqual("AA", seq2)
self.assertLessEqual(b"AA", seq1)
self.assertLessEqual(b"AA", seq2)
self.assertLessEqual(Seq("AA"), seq1)
self.assertLessEqual(Seq("AA"), seq2)
self.assertLessEqual(MutableSeq("AA"), seq1)
self.assertLessEqual(MutableSeq("AA"), seq2)
self.assertLessEqual("GC", seq1)
self.assertLessEqual("GC", seq2)
self.assertLessEqual(b"GC", seq1)
self.assertLessEqual(b"GC", seq2)
self.assertLessEqual(Seq("GC"), seq1)
self.assertLessEqual(Seq("GC"), seq2)
self.assertLessEqual(MutableSeq("GC"), seq1)
self.assertLessEqual(MutableSeq("GC"), seq2)
with self.assertRaises(UndefinedSequenceError):
seq1 <= Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 <= Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 <= Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 <= Seq(None, 10)
def test_gt(self):
seq1 = self.seq1a
seq2 = self.seq2a
self.assertGreater(seq2, seq1)
self.assertGreater("TT", seq1)
self.assertGreater(seq2, "TT")
self.assertGreater(b"TT", seq1)
self.assertGreater(seq2, b"TT")
self.assertGreater(Seq("TT"), seq1)
self.assertGreater(seq2, Seq("TT"))
self.assertGreater(MutableSeq("TT"), seq1)
self.assertGreater(seq2, MutableSeq("TT"))
self.assertGreater(seq1, "AA")
self.assertGreater(seq2, "AA")
self.assertGreater(seq1, b"AA")
self.assertGreater(seq2, b"AA")
self.assertGreater(seq1, Seq("AA"))
self.assertGreater(seq2, Seq("AA"))
self.assertGreater(seq1, MutableSeq("AA"))
self.assertGreater(seq2, MutableSeq("AA"))
self.assertGreater(seq1, "GC")
self.assertGreater(seq2, "GC")
self.assertGreater(seq1, b"GC")
self.assertGreater(seq2, b"GC")
self.assertGreater(seq1, Seq("GC"))
self.assertGreater(seq2, Seq("GC"))
self.assertGreater(seq1, MutableSeq("GC"))
self.assertGreater(seq2, MutableSeq("GC"))
with self.assertRaises(UndefinedSequenceError):
seq1 > Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 > Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 > Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 > Seq(None, 10)
def test_ge(self):
seq1 = self.seq1a
seq2 = self.seq2a
self.assertGreaterEqual(seq2, seq1)
self.assertGreaterEqual("TT", seq1)
self.assertGreaterEqual(seq2, "TT")
self.assertGreaterEqual(b"TT", seq1)
self.assertGreaterEqual(seq2, b"TT")
self.assertGreaterEqual(Seq("TT"), seq1)
self.assertGreaterEqual(seq2, Seq("TT"))
self.assertGreaterEqual(MutableSeq("TT"), seq1)
self.assertGreaterEqual(seq2, MutableSeq("TT"))
self.assertGreaterEqual(seq1, "AA")
self.assertGreaterEqual(seq2, "AA")
self.assertGreaterEqual(seq1, b"AA")
self.assertGreaterEqual(seq2, b"AA")
self.assertGreaterEqual(seq1, Seq("AA"))
self.assertGreaterEqual(seq2, Seq("AA"))
self.assertGreaterEqual(seq1, MutableSeq("AA"))
self.assertGreaterEqual(seq2, MutableSeq("AA"))
self.assertGreaterEqual(seq1, "GC")
self.assertGreaterEqual(seq2, "GC")
self.assertGreaterEqual(seq1, b"GC")
self.assertGreaterEqual(seq2, b"GC")
self.assertGreaterEqual(seq1, Seq("GC"))
self.assertGreaterEqual(seq2, Seq("GC"))
self.assertGreaterEqual(seq1, MutableSeq("GC"))
self.assertGreaterEqual(seq2, MutableSeq("GC"))
with self.assertRaises(UndefinedSequenceError):
seq1 >= Seq(None, len(seq1))
with self.assertRaises(UndefinedSequenceError):
seq2 >= Seq(None, len(seq2))
with self.assertRaises(UndefinedSequenceError):
seq1 >= Seq(None, 10)
with self.assertRaises(UndefinedSequenceError):
seq2 >= Seq(None, 10)
class TestBaseClassMethods(unittest.TestCase):
"""Test if methods from the base class are called correctly."""
def setUp(self):
path = "TwoBit/sequence.bigendian.2bit"
self.stream = open(path, "rb")
records = SeqIO.parse(self.stream, "twobit")
self.record1_twobit = next(records)
self.seq1_twobit = self.record1_twobit.seq
self.record2_twobit = next(records)
self.seq2_twobit = self.record2_twobit.seq
path = "TwoBit/sequence.fa"
records = SeqIO.parse(path, "fasta")
self.record1_fasta = next(records)
self.seq1_fasta = self.record1_fasta.seq
self.record2_fasta = next(records)
self.seq2_fasta = self.record2_fasta.seq
def tearDown(self):
self.stream.close()
def test_getitem(self):
self.assertEqual(self.seq1_twobit, self.seq1_fasta)
self.assertEqual(self.seq2_twobit, self.seq2_fasta)
self.assertEqual(self.seq1_twobit[:], self.seq1_fasta[:])
self.assertEqual(self.seq2_twobit[:], self.seq2_fasta[:])
self.assertEqual(self.seq1_twobit[30], self.seq1_fasta[30])
self.assertEqual(self.seq2_twobit[30], self.seq2_fasta[30])
self.assertEqual(self.seq1_twobit[-30], self.seq1_fasta[-30])
self.assertEqual(self.seq2_twobit[-30], self.seq2_fasta[-30])
self.assertEqual(self.record1_twobit.seq, self.record1_fasta.seq)
self.assertEqual(self.record2_twobit.seq, self.record2_fasta.seq)
self.assertEqual(self.record1_twobit[:].seq, self.record1_fasta[:].seq)
self.assertEqual(self.record2_twobit[:].seq, self.record2_fasta[:].seq)
self.assertEqual(self.record1_twobit[30], self.record1_fasta[30])
self.assertEqual(self.record2_twobit[30], self.record2_fasta[30])
self.assertEqual(self.record1_twobit[-30], self.record1_fasta[-30])
self.assertEqual(self.record2_twobit[-30], self.record2_fasta[-30])
def test_bytes(self):
b = bytes(self.seq1_twobit)
self.assertIsInstance(b, bytes)
self.assertEqual(len(b), 480)
self.assertEqual(b, bytes(self.seq1_fasta))
b = bytes(self.seq1_twobit[:10])
self.assertEqual(len(b), 10)
self.assertIsInstance(b, bytes)
self.assertEqual(b, b"GTATACCCCT")
def test_hash(self):
self.assertEqual(hash(self.seq1_twobit), hash(self.seq1_fasta))
def test_add(self):
self.assertIsInstance(self.seq1_twobit + "ABCD", Seq)
self.assertEqual(self.seq1_twobit + "ABCD", self.seq1_fasta + "ABCD")
self.assertIsInstance(self.record1_twobit + "ABCD", SeqRecord)
record1_twobit = self.record1_twobit + "ABCD"
record1_fasta = self.record1_fasta + "ABCD"
self.assertEqual(self.record1_twobit.seq, self.record1_fasta.seq)
def test_radd(self):
self.assertIsInstance("ABCD" + self.seq1_twobit, Seq)
self.assertEqual("ABCD" + self.seq1_twobit, "ABCD" + self.seq1_fasta)
self.assertIsInstance("ABCD" + self.record1_twobit, SeqRecord)
record1_twobit = "ABCD" + self.record1_twobit
record1_fasta = "ABCD" + self.record1_fasta
self.assertEqual(self.record1_twobit.seq, self.record1_fasta.seq)
def test_mul(self):
self.assertIsInstance(2 * self.seq1_twobit, Seq)
self.assertEqual(2 * self.seq1_twobit, 2 * self.seq1_fasta)
self.assertIsInstance(self.seq1_twobit * 2, Seq)
self.assertEqual(self.seq1_twobit * 2, self.seq1_fasta * 2)
def test_contains(self):
for seq in (
self.seq1_twobit,
self.seq1_fasta,
self.record1_twobit,
self.record1_fasta,
):
self.assertIn("ACCCCT", seq)
self.assertNotIn("ACGTACGT", seq)
def test_repr(self):
self.assertIsInstance(repr(self.seq1_twobit), str)
self.assertEqual(repr(self.seq1_twobit), repr(self.seq1_fasta))
def test_str(self):
self.assertIsInstance(str(self.seq1_twobit), str)
self.assertEqual(str(self.seq1_twobit), str(self.seq1_fasta))
def test_count(self):
self.assertEqual(self.seq1_twobit.count("CT"), self.seq1_fasta.count("CT"))
self.assertEqual(
self.seq1_twobit.count("CT", 75), self.seq1_fasta.count("CT", 75)
)
self.assertEqual(
self.seq1_twobit.count("CT", 125, 250),
self.seq1_fasta.count("CT", 125, 250),
)
self.assertEqual(
self.record1_twobit.count("CT"), self.record1_fasta.count("CT")
)
self.assertEqual(
self.record1_twobit.count("CT", 75), self.record1_fasta.count("CT", 75)
)
self.assertEqual(
self.record1_twobit.count("CT", 125, 250),
self.record1_fasta.count("CT", 125, 250),
)
def test_find(self):
self.assertEqual(self.seq1_twobit.find("CT"), self.seq1_fasta.find("CT"))
self.assertEqual(
self.seq1_twobit.find("CT", 75), self.seq1_fasta.find("CT", 75)
)
self.assertEqual(
self.seq1_twobit.find("CT", 75, 100), self.seq1_fasta.find("CT", 75, 100)
)
self.assertEqual(
self.seq1_twobit.find("CT", None, 100),
self.seq1_fasta.find("CT", None, 100),
)
def test_rfind(self):
self.assertEqual(self.seq1_twobit.rfind("CT"), self.seq1_fasta.rfind("CT"))
self.assertEqual(
self.seq1_twobit.rfind("CT", 450), self.seq1_fasta.rfind("CT", 450)
)
self.assertEqual(
self.seq1_twobit.rfind("CT", None, 100),
self.seq1_fasta.rfind("CT", None, 100),
)
self.assertEqual(
self.seq1_twobit.rfind("CT", 75, 100), self.seq1_fasta.rfind("CT", 75, 100)
)
def test_index(self):
self.assertEqual(self.seq1_twobit.index("CT"), self.seq1_fasta.index("CT"))
self.assertEqual(
self.seq1_twobit.index("CT", 75), self.seq1_fasta.index("CT", 75)
)
self.assertEqual(
self.seq1_twobit.index("CT", None, 100),
self.seq1_fasta.index("CT", None, 100),
)
for seq in (self.seq1_twobit, self.seq1_fasta):
self.assertRaises(ValueError, seq.index, "CT", 75, 100)
def test_rindex(self):
self.assertEqual(self.seq1_twobit.rindex("CT"), self.seq1_fasta.rindex("CT"))
self.assertEqual(
self.seq1_twobit.rindex("CT", None, 100),
self.seq1_fasta.rindex("CT", None, 100),
)
for seq in (self.seq1_twobit, self.seq1_fasta):
self.assertRaises(ValueError, seq.rindex, "CT", 450)
self.assertRaises(ValueError, seq.rindex, "CT", 75, 100)
def test_startswith(self):
for seq in (self.seq1_twobit, self.seq1_fasta):
self.assertTrue(seq.startswith("GTAT"))
self.assertTrue(seq.startswith("TGGG", start=10))
self.assertTrue(seq.startswith("TGGG", start=10, end=14))
self.assertFalse(seq.startswith("TGGG", start=10, end=12))
def test_endswith(self):
for seq in (self.seq1_twobit, self.seq1_fasta):
self.assertTrue(seq.endswith("ACCG"))
self.assertTrue(seq.endswith("ACCG", 476))
self.assertTrue(seq.endswith("GCAC", 472, 478))
self.assertFalse(seq.endswith("GCAC", 476, 478))
def test_split(self):
self.assertEqual(self.seq1_twobit.split(), self.seq1_fasta.split())
self.assertEqual(self.seq1_twobit.split("C"), self.seq1_fasta.split("C"))
self.assertEqual(self.seq1_twobit.split("C", 1), self.seq1_fasta.split("C", 1))
def test_rsplit(self):
self.assertEqual(self.seq1_twobit.rsplit(), self.seq1_fasta.rsplit())
self.assertEqual(self.seq1_twobit.rsplit("C"), self.seq1_fasta.rsplit("C"))
self.assertEqual(
self.seq1_twobit.rsplit("C", 1), self.seq1_fasta.rsplit("C", 1)
)
def test_strip(self):
self.assertEqual(self.seq1_twobit.strip("G"), self.seq1_fasta.strip("G"))
def test_lstrip(self, chars=None):
self.assertEqual(self.seq1_twobit.lstrip("G"), self.seq1_fasta.lstrip("G"))
def test_rstrip(self, chars=None):
self.assertEqual(self.seq1_twobit.rstrip("G"), self.seq1_fasta.rstrip("G"))
def test_upper(self):
seq1_twobit_upper = self.seq1_twobit.upper()
seq1_fasta_upper = self.seq1_fasta.upper()
self.assertEqual(seq1_twobit_upper, seq1_fasta_upper)
self.assertEqual(seq1_twobit_upper[140:210], seq1_fasta_upper[140:210])
seq2_twobit_upper = self.seq2_twobit.upper()
seq2_fasta_upper = self.seq2_fasta.upper()
self.assertEqual(seq2_twobit_upper, seq2_fasta_upper)
self.assertEqual(seq2_twobit_upper[140:210], seq2_fasta_upper[140:210])
def test_lower(self):
seq1_twobit_lower = self.seq1_twobit.lower()
seq1_fasta_lower = self.seq1_fasta.lower()
self.assertEqual(seq1_twobit_lower, seq1_fasta_lower)
self.assertEqual(seq1_twobit_lower[140:210], seq1_fasta_lower[140:210])
seq2_twobit_lower = self.seq2_twobit.lower()
seq2_fasta_lower = self.seq2_fasta.lower()
self.assertEqual(seq2_twobit_lower, seq2_fasta_lower)
self.assertEqual(seq2_twobit_lower[140:210], seq2_fasta_lower[140:210])
def test_isupper(self):
self.assertEqual(self.seq1_twobit.isupper(), self.seq1_fasta.isupper())
self.assertEqual(self.seq2_twobit.isupper(), self.seq2_fasta.isupper())
self.assertEqual(self.record1_twobit.isupper(), self.record1_fasta.isupper())
self.assertEqual(self.record2_twobit.isupper(), self.record2_fasta.isupper())
def test_islower(self):
self.assertEqual(self.seq1_twobit.islower(), self.seq1_fasta.islower())
self.assertEqual(self.seq2_twobit.islower(), self.seq2_fasta.islower())
self.assertEqual(self.record1_twobit.islower(), self.record1_fasta.islower())
self.assertEqual(self.record2_twobit.islower(), self.record2_fasta.islower())
def test_replace(self):
# seq.transcribe uses seq._data.replace
self.assertEqual(self.seq1_twobit.transcribe(), self.seq1_fasta.transcribe())
def test_translate(self):
# seq.reverse_complement uses seq._data.translate
self.assertEqual(
self.seq1_twobit.reverse_complement(), self.seq1_fasta.reverse_complement()
)
record1_twobit = self.record1_twobit.reverse_complement()
record1_fasta = self.record1_fasta.reverse_complement()
self.assertEqual(record1_twobit.seq, record1_fasta.seq)
def test_defined(self):
self.assertTrue(self.seq1_twobit.defined)
self.assertTrue(self.seq2_twobit.defined)
self.assertEqual(self.seq1_twobit.defined_ranges, ((0, len(self.seq1_twobit)),))
self.assertEqual(self.seq2_twobit.defined_ranges, ((0, len(self.seq2_twobit)),))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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