def setUp(self):
self.seq = Seq("CCCAAAATGTACTCCACTATCTGCTGATTTGGG", generic_dna)
self.feature = SeqFeature(FeatureLocation(6, 27),
type="gene",
strand=1)
self.feature_seq = self.seq[3:-3]
self.match = FeatureMatch(self.feature, self.feature_seq, 1, 3)
def test__init(self):
"Test FeatureMatch object creation"
# forward strand
m = self.match
self.assertEqual(m.direction, "forward")
self.assertEqual(str(m.dna), "ATGTACTCCACTATCTGCTGA")
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna), str(self.feature_seq.transcribe()))
self.assertEqual(
str(m.aas),
str(self.feature.extract(self.seq).translate(to_stop=True)))
# reverse strand
inv_seq = self.seq.reverse_complement()
feature_seq = inv_seq[3:-3]
inv_feature = SeqFeature(FeatureLocation(6, 27),
type="gene",
strand=-1)
m = FeatureMatch(inv_feature, feature_seq, -1, 3)
self.assertEqual(m.direction, "reverse")
self.assertEqual(str(m.dna),
str(feature_seq[3:-3].reverse_complement()))
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna),
str(feature_seq.transcribe().reverse_complement()))
self.assertEqual(
str(m.aas),
str(inv_feature.extract(inv_seq).translate(to_stop=True)))
def setUp(self):
self.seq = Seq("CCCAAAATGTACTCCACTATCTGCTGATTTGGG", generic_dna)
self.feature = SeqFeature(FeatureLocation(6, 27), type="gene", strand=1)
self.feature_seq = self.seq[3:-3]
self.match = FeatureMatch(self.feature, self.feature_seq, 1, 3)
class TestFeatureMatch(unittest2.TestCase):
def setUp(self):
self.seq = Seq("CCCAAAATGTACTCCACTATCTGCTGATTTGGG", generic_dna)
self.feature = SeqFeature(FeatureLocation(6, 27), type="gene", strand=1)
self.feature_seq = self.seq[3:-3]
self.match = FeatureMatch(self.feature, self.feature_seq, 1, 3)
def test__init(self):
"Test FeatureMatch object creation"
# forward strand
m = self.match
self.assertEqual(m.direction, "forward")
self.assertEqual(str(m.dna), "ATGTACTCCACTATCTGCTGA")
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna), str(self.feature_seq.transcribe()))
self.assertEqual(str(m.aas), str(self.feature.extract(self.seq).translate(to_stop=True)))
# reverse strand
inv_seq = self.seq.reverse_complement()
feature_seq = inv_seq[3:-3]
inv_feature = SeqFeature(FeatureLocation(6, 27), type="gene", strand=-1)
m = FeatureMatch(inv_feature, feature_seq, -1, 3)
self.assertEqual(m.direction, "reverse")
self.assertEqual(str(m.dna), str(feature_seq[3:-3].reverse_complement()))
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna), str(feature_seq.transcribe().reverse_complement()))
self.assertEqual(str(m.aas), str(inv_feature.extract(inv_seq).translate(to_stop=True)))
def test_get_fasta_header(self):
"Test FeatureMatch FASTA header creation"
expected = ">untagged"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['gene'] = ['fake']
expected = ">fake"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['locus_tag'] = ['FAKE_0001']
expected = ">FAKE_0001"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['product'] = ['Mup1']
expected = ">FAKE_0001|Mup1"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['protein_id'] = ['MUP_0001']
expected = ">FAKE_0001|Mup1|MUP_0001"
self.assertEqual(self.match.get_fasta_header(), expected)
def test__str_(self):
"Test FeatureMatch string representation"
expected = """Feature:
untagged
Strand: forward
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['gene'] = ["fake"]
expected = """Feature:
Tag: fake
Strand: forward
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['locus_tag'] = ['FAKE_0001']
expected = """Feature:
Tag: FAKE_0001
Strand: forward
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['product'] = ['Mup1']
expected = """Feature:
Tag: FAKE_0001
Strand: forward
Product: Mup1
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['protein_id'] = ['MUP_0001']
expected = """Feature:
Tag: FAKE_0001
Strand: forward
Product: Mup1
Protein ID: MUP_0001
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
def test_dna_fasta(self):
"Test FeatureMatch DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.dna)
self.assertMultiLineEqual(self.match.dna_fasta(), expected)
def test_long_dna_fasta(self):
"Test FeatureMatch long DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.long_dna)
self.assertMultiLineEqual(self.match.long_dna_fasta(), expected)
def test_mrna_fasta(self):
"Test FeatureMatch mRNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.mrna)
self.assertMultiLineEqual(self.match.mrna_fasta(), expected)
def test_protein_fasta(self):
"Test FeatureMatch protein FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.aas)
self.assertMultiLineEqual(self.match.protein_fasta(), expected)
def test_promotor_fasta(self):
"Test FeatureMatch promotor DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.promotor_region)
self.assertMultiLineEqual(self.match.promotor_fasta(), expected)
def test_terminator_fasta(self):
"Test FeatureMatch terminator DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.terminator_region)
self.assertMultiLineEqual(self.match.terminator_fasta(), expected)
class TestFeatureMatch(unittest.TestCase):
def setUp(self):
self.seq = Seq("CCCAAAATGTACTCCACTATCTGCTGATTTGGG", generic_dna)
self.feature = SeqFeature(FeatureLocation(6, 27),
type="gene",
strand=1)
self.feature_seq = self.seq[3:-3]
self.match = FeatureMatch(self.feature, self.feature_seq, 1, 3)
def test__init(self):
"Test FeatureMatch object creation"
# forward strand
m = self.match
self.assertEqual(m.direction, "forward")
self.assertEqual(str(m.dna), "ATGTACTCCACTATCTGCTGA")
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna), str(self.feature_seq.transcribe()))
self.assertEqual(
str(m.aas),
str(self.feature.extract(self.seq).translate(to_stop=True)))
# reverse strand
inv_seq = self.seq.reverse_complement()
feature_seq = inv_seq[3:-3]
inv_feature = SeqFeature(FeatureLocation(6, 27),
type="gene",
strand=-1)
m = FeatureMatch(inv_feature, feature_seq, -1, 3)
self.assertEqual(m.direction, "reverse")
self.assertEqual(str(m.dna),
str(feature_seq[3:-3].reverse_complement()))
self.assertEqual(str(m.long_dna), str(self.feature_seq))
self.assertEqual(str(m.promotor_region), "AAA")
self.assertEqual(str(m.terminator_region), "TTT")
self.assertEqual(str(m.mrna),
str(feature_seq.transcribe().reverse_complement()))
self.assertEqual(
str(m.aas),
str(inv_feature.extract(inv_seq).translate(to_stop=True)))
def test_get_fasta_header(self):
"Test FeatureMatch FASTA header creation"
expected = ">untagged"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['gene'] = ['fake']
expected = ">fake"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['locus_tag'] = ['FAKE_0001']
expected = ">FAKE_0001"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['product'] = ['Mup1']
expected = ">FAKE_0001|Mup1"
self.assertEqual(self.match.get_fasta_header(), expected)
self.match.feature.qualifiers['protein_id'] = ['MUP_0001']
expected = ">FAKE_0001|Mup1|MUP_0001"
self.assertEqual(self.match.get_fasta_header(), expected)
def test__str_(self):
"Test FeatureMatch string representation"
expected = """Feature:
untagged
Strand: forward
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['gene'] = ["fake"]
expected = """Feature:
Tag: fake
Strand: forward
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['locus_tag'] = ['FAKE_0001']
expected = """Feature:
Tag: FAKE_0001
Strand: forward
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['product'] = ['Mup1']
expected = """Feature:
Tag: FAKE_0001
Strand: forward
Product: Mup1
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
self.match.feature.qualifiers['protein_id'] = ['MUP_0001']
expected = """Feature:
Tag: FAKE_0001
Strand: forward
Product: Mup1
Protein ID: MUP_0001
DNA: ATGTACTCCACTATCTGCTGA
mRNA: AAAAUGUACUCCACUAUCUGCUGAUUU
Protein: MYSTIC"""
self.assertMultiLineEqual(str(self.match), expected)
def test_dna_fasta(self):
"Test FeatureMatch DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.dna)
self.assertMultiLineEqual(self.match.dna_fasta(), expected)
def test_long_dna_fasta(self):
"Test FeatureMatch long DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(),
self.match.long_dna)
self.assertMultiLineEqual(self.match.long_dna_fasta(), expected)
def test_mrna_fasta(self):
"Test FeatureMatch mRNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.mrna)
self.assertMultiLineEqual(self.match.mrna_fasta(), expected)
def test_protein_fasta(self):
"Test FeatureMatch protein FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(), self.match.aas)
self.assertMultiLineEqual(self.match.protein_fasta(), expected)
def test_promotor_fasta(self):
"Test FeatureMatch promotor DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(),
self.match.promotor_region)
self.assertMultiLineEqual(self.match.promotor_fasta(), expected)
def test_terminator_fasta(self):
"Test FeatureMatch terminator DNA FASTA output"
expected = "%s\n%s" % (self.match.get_fasta_header(),
self.match.terminator_region)
self.assertMultiLineEqual(self.match.terminator_fasta(), expected)