def test_count(self):
self.assertEqual(6, self.s.count("?"))
self.assertEqual(3, self.s.count("??"))
self.assertEqual(0, Seq.UnknownSeq(6, character="N").count("?"))
self.assertEqual(0, Seq.UnknownSeq(6, character="N").count("??"))
self.assertEqual(4, Seq.UnknownSeq(6, character="?").count("?", start=2))
self.assertEqual(2, Seq.UnknownSeq(6, character="?").count("??", start=2))
def test_ungap(self):
seq = Seq.UnknownSeq(7,
alphabet=Alphabet.Gapped(Alphabet.DNAAlphabet(),
"-"))
self.assertEqual("NNNNNNN", str(seq.ungap("-")))
seq = Seq.UnknownSeq(20,
alphabet=Alphabet.Gapped(Alphabet.DNAAlphabet(),
"-"),
character='-')
self.assertEqual("", seq.ungap("-"))
def parse(self):
with open(self._file) as handle:
genbank = SeqRecord(Seq.UnknownSeq(0))
header_pattern = re.compile(
r"ref\|(?P<id>.*?)\|:(?P<start>[0-9]+)-(?P<end>[0-9]+)\|(?P<description>.*?)\|\s*\[gene=(?P<gene>\S+)\]\s*\[locus_tag=(?P<locus_tag>\S+)\]\s*"
)
first = True
for record in SeqIO.parse(handle, "fasta"):
header = record.description
match = header_pattern.match(header)
if not match:
self.errors.append("Invalid header: >" + header)
continue
if first:
first = False
genbank.id = match.group("id")
genbank.name = match.group("id")
feature = SeqFeature(FeatureLocation(int(match.group("start")),
int(match.group("end"))),
type="gene")
feature.qualifiers = {
"locus_tag": match.group("locus_tag"),
"gene": match.group("gene"),
"note": match.group("description"),
"sequence": record.seq
}
genbank.features.append(feature)
return genbank
return None
def test_construction(self):
self.assertEqual("??????", str(Seq.UnknownSeq(6)))
self.assertEqual("NNNNNN", str(Seq.UnknownSeq(6, character="N")))
self.assertEqual("XXXXXX", str(Seq.UnknownSeq(6, character="X")))
self.assertEqual("??????", str(Seq.UnknownSeq(6, character="?")))
with self.assertRaises(ValueError):
Seq.UnknownSeq(-10)
with self.assertRaises(ValueError):
Seq.UnknownSeq(6, character="??")
def test_construction(self):
self.assertEqual("??????", str(Seq.UnknownSeq(6)))
self.assertEqual("NNNNNN", str(Seq.UnknownSeq(6,
Alphabet.generic_dna)))
self.assertEqual("XXXXXX",
str(Seq.UnknownSeq(6, Alphabet.generic_protein)))
self.assertEqual("??????", str(Seq.UnknownSeq(6, character="?")))
with self.assertRaises(ValueError):
Seq.UnknownSeq(-10)
with self.assertRaises(ValueError):
Seq.UnknownSeq(6, character="??")
def test_unknownseq_construction(self):
self.assertEqual("??????", Seq.UnknownSeq(6))
self.assertEqual("NNNNNN", Seq.UnknownSeq(6, character="N"))
self.assertEqual("XXXXXX", Seq.UnknownSeq(6, character="X"))
self.assertEqual("??????", Seq.UnknownSeq(6, character="?"))
with self.assertRaises(ValueError):
"??????" == self.u
with self.assertRaises(ValueError):
self.u == "??????"
with self.assertRaises(ValueError):
Seq.UnknownSeq(-10)
with self.assertRaises(ValueError):
Seq.Seq(None, length=-10)
with self.assertRaises(ValueError):
Seq.UnknownSeq(6, character="??")
def test_upper(self):
seq = Seq.UnknownSeq(6, Alphabet.generic_dna)
self.assertEqual("NNNNNN", str(seq.upper()))
def setUp(self):
self.s = Seq.UnknownSeq(6)
def test_lower(self):
seq = Seq.UnknownSeq(6, character="N")
self.assertEqual("nnnnnn", seq.lower())
self.assertRaises(ValueError, self.u.lower)
def test_upper(self):
seq = Seq.UnknownSeq(6, character="N")
self.assertEqual("NNNNNN", seq.upper())
self.assertRaises(ValueError, self.u.upper)
def setUp(self):
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
self.s = Seq.UnknownSeq(6)
self.u = Seq.Seq(None, length=6)
def setUp(self):
self.s = Seq.UnknownSeq(6)
self.u = Seq.Seq(None, length=6)
def test_lower(self):
seq = Seq.UnknownSeq(6, character="N")
self.assertEqual("nnnnnn", str(seq.lower()))
def test_add_method(self):
seq1 = Seq.UnknownSeq(3, character="N")
self.assertEqual("??????NNN", str(self.s + seq1))
seq2 = Seq.UnknownSeq(3, character="N")
self.assertEqual("NNNNNN", str(seq1 + seq2))
def test_add_method(self):
seq1 = Seq.UnknownSeq(3, Alphabet.generic_dna)
self.assertEqual("??????NNN", str(self.s + seq1))
seq2 = Seq.UnknownSeq(3, Alphabet.generic_dna)
self.assertEqual("NNNNNN", str(seq1 + seq2))
def test_complement_of_protein(self):
"""Test reverse complement shouldn't work on a protein!"""
seq = Seq.UnknownSeq(6, Alphabet.generic_protein)
with self.assertRaises(ValueError):
seq.complement()
def test_translation_of_proteins(self):
seq = Seq.UnknownSeq(6, IUPAC.protein)
self.assertRaises(ValueError, seq.translate)
def test_reverse_complement_of_protein(self):
seq = Seq.UnknownSeq(6, Alphabet.generic_protein)
self.assertRaises(ValueError, seq.reverse_complement)
def test_upper(self):
seq = Seq.UnknownSeq(6, character="N")
self.assertEqual("NNNNNN", str(seq.upper()))
def test_lower(self):
seq = Seq.UnknownSeq(6, Alphabet.generic_dna)
self.assertEqual("nnnnnn", str(seq.lower()))
def test_ungap(self):
seq = Seq.UnknownSeq(7, character="N")
self.assertEqual("NNNNNNN", str(seq.ungap("-")))
seq = Seq.UnknownSeq(20, character="-")
self.assertEqual("", seq.ungap("-"))
def test_ungap(self):
seq = Seq.UnknownSeq(7, alphabet=Alphabet.generic_dna)
self.assertEqual("NNNNNNN", str(seq.ungap("-")))
seq = Seq.UnknownSeq(20, alphabet=Alphabet.generic_dna, character="-")
self.assertEqual("", seq.ungap("-"))
