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# Copyright 2009-2017 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""SeqFeature related tests for SeqRecord objects from Bio.SeqIO.
Initially this takes matched tests of GenBank and FASTA files from the NCBI
and confirms they are consistent using our different parsers.
"""
import unittest
from Bio import SeqIO
from Bio.Alphabet import generic_dna, generic_protein
from Bio.Seq import Seq, MutableSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, ExactPosition
from Bio.SeqFeature import WithinPosition, BeforePosition, AfterPosition, OneOfPosition
class SeqRecordCreation(unittest.TestCase):
"""Test basic creation of SeqRecords."""
def test_annotations(self):
"""Pass in annotations to SeqRecords"""
rec = SeqRecord(Seq("ACGT", generic_dna),
id="Test", name="Test", description="Test")
self.assertEqual(rec.annotations, {})
rec = SeqRecord(Seq("ACGT", generic_dna),
id="Test", name="Test", description="Test",
annotations={"test": ["a test"]})
self.assertEqual(rec.annotations["test"], ["a test"])
def test_letter_annotations(self):
"""Pass in letter annotations to SeqRecords"""
rec = SeqRecord(Seq("ACGT", generic_dna),
id="Test", name="Test", description="Test")
self.assertEqual(rec.annotations, {})
rec = SeqRecord(Seq("ACGT", generic_dna),
id="Test", name="Test", description="Test",
letter_annotations={"test": [1, 2, 3, 4]})
self.assertEqual(rec.letter_annotations["test"], [1, 2, 3, 4])
# Now try modifying it to a bad value...
try:
rec.letter_annotations["bad"] = "abc"
self.fail("Adding a bad letter_annotation should fail!")
except (TypeError, ValueError) as e:
pass
# Now try setting it afterwards to a bad value...
rec = SeqRecord(Seq("ACGT", generic_dna),
id="Test", name="Test", description="Test")
try:
rec.letter_annotations = {"test": [1, 2, 3]}
self.fail("Changing to bad letter_annotations should fail!")
except (TypeError, ValueError) as e:
pass
# Now try setting it at creation time to a bad value...
try:
rec = SeqRecord(Seq("ACGT", generic_dna),
id="Test", name="Test", description="Test",
letter_annotations={"test": [1, 2, 3]})
self.fail("Wrong length letter_annotations should fail!")
except (TypeError, ValueError) as e:
pass
def test_replacing_seq(self):
"""Replacing .seq if .letter_annotation present."""
rec = SeqRecord(Seq("ACGT", generic_dna),
id="Test", name="Test", description="Test",
letter_annotations={"example": [1, 2, 3, 4]})
try:
rec.seq = Seq("ACGTACGT", generic_dna)
self.fail("Changing .seq length with letter_annotations present should fail!")
except ValueError as e:
self.assertEqual(str(e), "You must empty the letter annotations first!")
# Check we can replace IF the length is the same
self.assertEqual(str(rec.seq), "ACGT")
self.assertEqual(rec.letter_annotations, {"example": [1, 2, 3, 4]})
rec.seq = Seq("NNNN", generic_dna)
self.assertEqual(str(rec.seq), "NNNN")
self.assertEqual(rec.letter_annotations, {"example": [1, 2, 3, 4]})
def test_valid_id(self):
with self.assertRaises(TypeError):
SeqRecord(Seq("ACGT", generic_dna), id=dict())
def test_valid_name(self):
with self.assertRaises(TypeError):
SeqRecord(Seq("ACGT", generic_dna), name=dict())
def test_valid_description(self):
with self.assertRaises(TypeError):
SeqRecord(Seq("ACGT", generic_dna), description=dict())
def test_valid_dbxrefs(self):
with self.assertRaises(TypeError):
SeqRecord(Seq("ACGT", generic_dna), dbxrefs=dict())
def test_valid_annotations(self):
with self.assertRaises(TypeError):
SeqRecord(Seq("ACGT", generic_dna), annotations=list())
def test_valid_features(self):
with self.assertRaises(TypeError):
SeqRecord(Seq("ACGT", generic_dna), features=dict())
class SeqRecordMethods(unittest.TestCase):
"""Test SeqRecord methods."""
def setUp(self):
f0 = SeqFeature(FeatureLocation(0, 26), type="source",
qualifiers={"mol_type": ["fake protein"]})
f1 = SeqFeature(FeatureLocation(0, ExactPosition(10)))
f2 = SeqFeature(FeatureLocation(WithinPosition(12, left=12, right=15), BeforePosition(22)))
f3 = SeqFeature(FeatureLocation(AfterPosition(16),
OneOfPosition(26, [ExactPosition(25), AfterPosition(26)])))
self.record = SeqRecord(Seq("ABCDEFGHIJKLMNOPQRSTUVWZYX", generic_protein),
id="TestID", name="TestName", description="TestDescr",
dbxrefs=["TestXRef"], annotations={"k": "v"},
letter_annotations={"fake": "X" * 26},
features=[f0, f1, f2, f3])
def test_iter(self):
for amino in self.record:
self.assertEqual("A", amino)
break
def test_contains(self):
self.assertIn(Seq("ABC", generic_protein), self.record)
def test_str(self):
expected = """
ID: TestID
Name: TestName
Description: TestDescr
Database cross-references: TestXRef
Number of features: 4
/k=v
Per letter annotation for: fake
Seq('ABCDEFGHIJKLMNOPQRSTUVWZYX', ProteinAlphabet())"""
self.assertEqual(expected.lstrip(), str(self.record))
def test_repr(self):
expected = "SeqRecord(seq=Seq('ABCDEFGHIJKLMNOPQRSTUVWZYX', ProteinAlphabet()), " \
"id='TestID', name='TestName', description='TestDescr', dbxrefs=['TestXRef'])"
self.assertEqual(expected, repr(self.record))
def test_format(self):
expected = ">TestID TestDescr\nABCDEFGHIJKLMNOPQRSTUVWZYX\n"
self.assertEqual(expected, self.record.format('fasta'))
def test_upper(self):
self.assertEqual("ABCDEFGHIJKLMNOPQRSTUVWZYX", str(self.record.lower().upper().seq))
def test_lower(self):
self.assertEqual("abcdefghijklmnopqrstuvwzyx", str(self.record.lower().seq))
def test_slicing(self):
self.assertEqual("B", self.record[1])
self.assertEqual("BC", self.record[1:3].seq)
with self.assertRaises(ValueError):
c = self.record['a'].seq
def test_slice_variants(self):
"""Simple slices using different start/end values"""
for start in list(range(-30, 30)) + [None]:
for end in list(range(-30, 30)) + [None]:
if start is None and end is None:
continue
rec = self.record[start:end]
seq = self.record.seq[start:end]
seq_str = str(self.record.seq)[start:end]
self.assertEqual(seq_str, str(seq))
self.assertEqual(seq_str, str(rec.seq))
self.assertEqual("X" * len(seq_str), rec.letter_annotations["fake"])
def test_slice_simple(self):
"""Simple slice"""
rec = self.record
self.assertEqual(len(rec), 26)
left = rec[:10]
self.assertEqual(str(left.seq), str(rec.seq[:10]))
right = rec[-10:]
self.assertEqual(str(right.seq), str(rec.seq[-10:]))
mid = rec[12:22]
self.assertEqual(str(mid.seq), str(rec.seq[12:22]))
for sub in [left, right, mid]:
self.assertEqual(len(sub), 10)
self.assertEqual(sub.id, "TestID")
self.assertEqual(sub.name, "TestName")
self.assertEqual(sub.description, "TestDescr")
self.assertEqual(sub.letter_annotations, {"fake": "X" * 10})
self.assertEqual(sub.dbxrefs, []) # May change this...
self.assertEqual(sub.annotations, {}) # May change this...
self.assertEqual(len(sub.features), 1)
# By construction, each feature matches the full sliced region:
self.assertEqual(str(sub.features[0].extract(sub.seq)), str(sub.seq))
self.assertEqual(sub.features[0].extract(str(sub.seq)), str(sub.seq))
def test_slice_zero(self):
"""Zero slice"""
rec = self.record
self.assertEqual(len(rec), 26)
self.assertEqual(len(rec[2:-2]), 22)
self.assertEqual(len(rec[5:2]), 0)
self.assertEqual(len(rec[5:2][2:-2]), 0)
def test_add_simple(self):
"""Simple addition"""
rec = self.record + self.record
self.assertEqual(len(rec), 52)
self.assertEqual(rec.id, "TestID")
self.assertEqual(rec.name, "TestName")
self.assertEqual(rec.description, "TestDescr")
self.assertEqual(rec.dbxrefs, ["TestXRef"])
self.assertEqual(rec.annotations, {"k": "v"})
self.assertEqual(rec.letter_annotations, {"fake": "X" * 52})
self.assertEqual(len(rec.features), 2 * len(self.record.features))
def test_add_seq(self):
"""Simple addition of Seq or string"""
for other in [Seq("BIO"), "BIO"]:
rec = self.record + other # will use SeqRecord's __add__ method
self.assertEqual(len(rec), 26 + 3)
self.assertEqual(str(rec.seq), str(self.record.seq) + "BIO")
self.assertEqual(rec.id, "TestID")
self.assertEqual(rec.name, "TestName")
self.assertEqual(rec.description, "TestDescr")
self.assertEqual(rec.dbxrefs, ["TestXRef"])
self.assertEqual(rec.annotations, {"k": "v"})
self.assertEqual(rec.letter_annotations, {})
self.assertEqual(len(rec.features), len(self.record.features))
self.assertEqual(rec.features[0].type, "source")
self.assertEqual(rec.features[0].location.nofuzzy_start, 0)
self.assertEqual(rec.features[0].location.nofuzzy_end, 26) # not +3
def test_add_seqrecord(self):
"""Simple left addition of SeqRecord from genbank file."""
other = SeqIO.read("GenBank/dbsource_wrap.gb", "gb")
other.dbxrefs = ["dummy"]
rec = self.record + other
self.assertEqual(len(rec), len(self.record) + len(other))
self.assertEqual(str(rec.seq), str(self.record.seq) + str(other.seq))
self.assertEqual(rec.id, "<unknown id>")
self.assertEqual(rec.name, "<unknown name>")
self.assertEqual(rec.description, "<unknown description>")
self.assertEqual(rec.dbxrefs, ["TestXRef", "dummy"])
self.assertEqual(len(rec.annotations), 0)
self.assertEqual(len(rec.letter_annotations), 0)
self.assertEqual(len(rec.features),
len(self.record.features) + len(other.features))
self.assertEqual(rec.features[0].type, "source")
self.assertEqual(rec.features[0].location.nofuzzy_start, 0)
self.assertEqual(rec.features[0].location.nofuzzy_end, len(self.record)) # not +3
i = len(self.record.features)
self.assertEqual(rec.features[i].type, "source")
self.assertEqual(rec.features[i].location.nofuzzy_start, len(self.record))
self.assertEqual(rec.features[i].location.nofuzzy_end, len(rec))
def test_add_seq_left(self):
"""Simple left addition of Seq or string"""
for other in [Seq("BIO"), "BIO"]:
rec = other + self.record # will use SeqRecord's __radd__ method
self.assertEqual(len(rec), 26 + 3)
self.assertEqual(str(rec.seq), "BIO" + str(self.record.seq))
self.assertEqual(rec.id, "TestID")
self.assertEqual(rec.name, "TestName")
self.assertEqual(rec.description, "TestDescr")
self.assertEqual(rec.dbxrefs, ["TestXRef"])
self.assertEqual(rec.annotations, {"k": "v"})
self.assertEqual(rec.letter_annotations, {})
self.assertEqual(len(rec.features), len(self.record.features))
self.assertEqual(rec.features[0].type, "source")
self.assertEqual(rec.features[0].location.nofuzzy_start, 3)
self.assertEqual(rec.features[0].location.nofuzzy_end, 26 + 3)
def test_slice_add_simple(self):
"""Simple slice and add"""
for cut in range(27):
rec = self.record[:cut] + self.record[cut:]
self.assertEqual(str(rec.seq), str(self.record.seq))
self.assertEqual(len(rec), 26)
self.assertEqual(rec.id, "TestID")
self.assertEqual(rec.name, "TestName")
self.assertEqual(rec.description, "TestDescr")
self.assertEqual(rec.dbxrefs, []) # May change this...
self.assertEqual(rec.annotations, {}) # May change this...
self.assertEqual(rec.letter_annotations, {"fake": "X" * 26})
self.assertTrue(len(rec.features) <= len(self.record.features))
def test_slice_add_shift(self):
"""Simple slice and add to shift"""
for cut in range(27):
rec = self.record[cut:] + self.record[:cut]
self.assertEqual(str(rec.seq), str(self.record.seq[cut:] + self.record.seq[:cut]))
self.assertEqual(len(rec), 26)
self.assertEqual(rec.id, "TestID")
self.assertEqual(rec.name, "TestName")
self.assertEqual(rec.description, "TestDescr")
self.assertEqual(rec.dbxrefs, []) # May change this...
self.assertEqual(rec.annotations, {}) # May change this...
self.assertEqual(rec.letter_annotations, {"fake": "X" * 26})
self.assertTrue(len(rec.features) <= len(self.record.features))
class SeqRecordMethodsMore(unittest.TestCase):
"""Test SeqRecord methods cont."""
# This class does not have a setUp defining self.record
def test_reverse_complement_seq(self):
s = SeqRecord(Seq("ACTG"), id="TestID", name="TestName",
description="TestDescription", dbxrefs=["TestDbxrefs"],
features=[SeqFeature(FeatureLocation(0, 3), type="Site")],
annotations={'organism': 'bombyx'},
letter_annotations={'test': 'abcd'})
rc = s.reverse_complement(id=True, name=True, description=True,
dbxrefs=True, features=True, annotations=True,
letter_annotations=True)
self.assertEqual("CAGT", str(rc.seq))
self.assertEqual("TestID", rc.id)
self.assertEqual("TestID", s.reverse_complement(id="TestID").id)
self.assertEqual("TestName", rc.name)
self.assertEqual("TestName", s.reverse_complement(name="TestName").name)
self.assertEqual("TestDescription", rc.description)
self.assertEqual("TestDescription",
s.reverse_complement(description="TestDescription").description)
self.assertEqual(["TestDbxrefs"], rc.dbxrefs)
self.assertEqual(["TestDbxrefs"],
s.reverse_complement(dbxrefs=["TestDbxrefs"]).dbxrefs)
self.assertEqual("[SeqFeature(FeatureLocation(ExactPosition(1), ExactPosition(4)), type='Site')]",
repr(rc.features))
rc2 = s.reverse_complement(features=[SeqFeature(FeatureLocation(1, 4), type="Site")])
self.assertEqual("[SeqFeature(FeatureLocation(ExactPosition(1), ExactPosition(4)), type='Site')]",
repr(rc2.features))
self.assertEqual({'organism': 'bombyx'}, rc.annotations)
self.assertEqual({'organism': 'bombyx'},
s.reverse_complement(annotations={'organism': 'bombyx'}).annotations)
self.assertEqual({'test': 'dcba'}, rc.letter_annotations)
self.assertEqual({'test': 'abcd'},
s.reverse_complement(letter_annotations={'test': 'abcd'}).letter_annotations)
def test_reverse_complement_mutable_seq(self):
s = SeqRecord(MutableSeq("ACTG"))
self.assertEqual("CAGT", str(s.reverse_complement().seq))
def test_translate(self):
s = SeqRecord(Seq("ATGGTGTAA"), id="TestID", name="TestName",
description="TestDescription", dbxrefs=["TestDbxrefs"],
features=[SeqFeature(FeatureLocation(0, 3), type="Site")],
annotations={'organism': 'bombyx'},
letter_annotations={'test': 'abcdefghi'})
t = s.translate()
self.assertEqual(t.seq, "MV*")
self.assertEqual(t.id, "<unknown id>")
self.assertEqual(t.name, "<unknown name>")
self.assertEqual(t.description, "<unknown description>")
self.assertFalse(t.dbxrefs)
self.assertFalse(t.features)
self.assertFalse(t.annotations)
self.assertFalse(t.letter_annotations)
t = s.translate(cds=True, id=True, name=True, description=True,
dbxrefs=True, annotations=True)
self.assertEqual(t.seq, "MV")
self.assertEqual(t.id, "TestID")
self.assertEqual(t.name, "TestName")
self.assertEqual(t.description, "TestDescription")
self.assertEqual(t.dbxrefs, ["TestDbxrefs"])
self.assertFalse(t.features)
self.assertEqual(t.annotations, {'organism': 'bombyx'})
self.assertFalse(t.letter_annotations)
def test_lt_exception(self):
def lt():
SeqRecord(Seq("A")) < SeqRecord(Seq("A"))
self.assertRaises(NotImplementedError, lt)
def test_le_exception(self):
def le():
SeqRecord(Seq("A")) <= SeqRecord(Seq("A"))
self.assertRaises(NotImplementedError, le)
def test_eq_exception(self):
def equality():
SeqRecord(Seq("A")) == SeqRecord(Seq("A"))
self.assertRaises(NotImplementedError, equality)
def test_ne_exception(self):
def notequality():
SeqRecord(Seq("A")) != SeqRecord(Seq("A"))
self.assertRaises(NotImplementedError, notequality)
def test_gt_exception(self):
def gt():
SeqRecord(Seq("A")) > SeqRecord(Seq("A"))
self.assertRaises(NotImplementedError, gt)
def test_ge_exception(self):
def ge():
SeqRecord(Seq("A")) >= SeqRecord(Seq("A"))
self.assertRaises(NotImplementedError, ge)
class TestTranslation(unittest.TestCase):
def setUp(self):
self.s = SeqRecord(Seq("ATGGTGTAA"), id="TestID", name="TestName",
description="TestDescription", dbxrefs=["TestDbxrefs"],
features=[SeqFeature(FeatureLocation(0, 3), type="Site")],
annotations={'organism': 'bombyx'},
letter_annotations={'test': 'abcdefghi'})
def test_defaults(self):
t = self.s.translate()
self.assertEqual(t.seq, "MV*")
self.assertEqual(t.id, "<unknown id>")
self.assertEqual(t.name, "<unknown name>")
self.assertEqual(t.description, "<unknown description>")
self.assertFalse(t.dbxrefs)
self.assertFalse(t.features)
self.assertFalse(t.annotations)
self.assertFalse(t.letter_annotations)
def test_preserve(self):
t = self.s.translate(cds=True, id=True, name=True, description=True,
dbxrefs=True, annotations=True)
self.assertEqual(t.seq, "MV")
self.assertEqual(t.id, "TestID")
self.assertEqual(t.name, "TestName")
self.assertEqual(t.description, "TestDescription")
self.assertEqual(t.dbxrefs, ["TestDbxrefs"])
self.assertFalse(t.features)
self.assertEqual(t.annotations, {'organism': 'bombyx'})
self.assertFalse(t.letter_annotations)
# Should not preserve these
self.assertRaises(TypeError, self.s.translate, features=True)
self.assertRaises(TypeError, self.s.translate, letter_annotations=True)
def test_new_annot(self):
t = self.s.translate(1, to_stop=True, gap="-",
id="Foo", name="Bar", description="Baz", dbxrefs=["Nope"],
features=[SeqFeature(FeatureLocation(0, 3), type="Site")],
annotations={"a": "team"},
letter_annotations={"aa": ["Met", "Val"]})
self.assertEqual(t.seq, "MV")
self.assertEqual(t.id, "Foo")
self.assertEqual(t.name, "Bar")
self.assertEqual(t.description, "Baz")
self.assertEqual(t.dbxrefs, ["Nope"])
self.assertEqual(len(t.features), 1)
self.assertEqual(t.annotations, {'a': 'team'})
self.assertEqual(t.letter_annotations, {"aa": ["Met", "Val"]})
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)