Python MutableSeq.complement方法代码示例

# 需要导入模块: from Bio.Seq import MutableSeq [as 别名]
# 或者: from Bio.Seq.MutableSeq import complement [as 别名]

#.........这里部分代码省略.........
                         self.mutable_s)

    def test_inserting(self):
        self.mutable_s.insert(4, "G")
        self.assertEqual(MutableSeq("TCAAGAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_popping_last_item(self):
        self.assertEqual("G", self.mutable_s.pop())

    def test_remove_items(self):
        self.mutable_s.remove("G")
        self.assertEqual(MutableSeq("TCAAAAGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s, "Remove first G")

        self.assertRaises(ValueError, self.mutable_s.remove, 'Z')

    def test_count(self):
        self.assertEqual(7, self.mutable_s.count("A"))
        self.assertEqual(2, self.mutable_s.count("AA"))

    def test_index(self):
        self.assertEqual(2, self.mutable_s.index("A"))
        self.assertRaises(ValueError, self.mutable_s.index, "8888")

    def test_reverse(self):
        """Test using reverse method"""
        self.mutable_s.reverse()
        self.assertEqual(MutableSeq("GTACTACGTAGGAAAACT", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_reverse_with_stride(self):
        """Test reverse using -1 stride"""
        self.assertEqual(MutableSeq("GTACTACGTAGGAAAACT", IUPAC.ambiguous_dna),
                         self.mutable_s[::-1])

    def test_complement(self):
        self.mutable_s.complement()
        self.assertEqual(str("AGTTTTCCTACGTAGTAC"), str(self.mutable_s))

    def test_complement_rna(self):
        seq = Seq.MutableSeq("AUGaaaCUG", IUPAC.unambiguous_rna)
        seq.complement()
        self.assertEqual(str("UACuuuGAC"), str(seq))

    def test_complement_mixed_aphabets(self):
        seq = Seq.MutableSeq("AUGaaaCTG")
        with self.assertRaises(ValueError):
            seq.complement()

    def test_complement_rna_string(self):
        seq = Seq.MutableSeq("AUGaaaCUG")
        seq.complement()
        self.assertEqual('UACuuuGAC', str(seq))

    def test_complement_dna_string(self):
        seq = Seq.MutableSeq("ATGaaaCTG")
        seq.complement()
        self.assertEqual('TACtttGAC', str(seq))

    def test_reverse_complement(self):
        self.mutable_s.reverse_complement()
        self.assertEqual("CATGATGCATCCTTTTGA", str(self.mutable_s))

    def test_reverse_complement_of_protein(self):
        seq = Seq.MutableSeq("ACTGTCGTCT", Alphabet.generic_protein)
        with self.assertRaises(ValueError):
            seq.reverse_complement()

    def test_to_string_method(self):
        """This method is currently deprecated, probably will need to remove this test soon"""
        with warnings.catch_warnings(record=True):
            self.mutable_s.tostring()

    def test_extend_method(self):
        self.mutable_s.extend("GAT")
        self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGGAT", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_extend_with_mutable_seq(self):
        self.mutable_s.extend(MutableSeq("TTT", IUPAC.ambiguous_dna))
        self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGTTT", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_delete_stride_slice(self):
        del self.mutable_s[4:6 - 1]
        self.assertEqual(MutableSeq("TCAAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_extract_third_nucleotide(self):
        """Test extracting every third nucleotide (slicing with stride 3)"""
        self.assertEqual(MutableSeq("TAGTAA", IUPAC.ambiguous_dna), self.mutable_s[0::3])
        self.assertEqual(MutableSeq("CAGGTT", IUPAC.ambiguous_dna), self.mutable_s[1::3])
        self.assertEqual(MutableSeq("AAACCG", IUPAC.ambiguous_dna), self.mutable_s[2::3])

    def test_set_wobble_codon_to_n(self):
        """Test setting wobble codon to N (set slice with stride 3)"""
        self.mutable_s[2::3] = "N" * len(self.mutable_s[2::3])
        self.assertEqual(MutableSeq("TCNAANGGNTGNATNATN", IUPAC.ambiguous_dna),
                         self.mutable_s)

# 需要导入模块: from Bio.Seq import MutableSeq [as 别名]
# 或者: from Bio.Seq.MutableSeq import complement [as 别名]
print len(seq)
#seq[0]='C'	#aren't mutables
st=str(seq)		#toString
print st

#tipo de dato secuencia editable
from Bio.Seq import MutableSeq
mut_seq=seq.tomutable()	#convertirlo a tipo seq mutable
print mut_seq
mut_seq[0]='C'
print mut_seq
mut_seq=MutableSeq('ATGCCG',IUPAC.IUPACUnambiguousDNA())
#has methods as a list: append(), insert(), pop(), remove()
mut_seq[1:3]='TTT'
mut_seq.reverse()
mut_seq.complement()
print mut_seq
mut_seq.reverse_complement()
print mut_seq

#tipo de dato metadatos de secuencia
from Bio.SeqRecord import SeqRecord
seqrec=SeqRecord(seq,id='001', name='My Secuencia')
#2 main attributes:
#	id: string identifier, optional, recommended
#	seq: Seq object, required
#additional attributes
#	name, description: name and more info of sequence
#	dbxrefs: list of strings, each string an id of a DB
#	features: list of SeqFeature objects, those found in Genbank records
#	annotations: dictionary with further info, can't be set on initialization