def test_complement_ambiguous_rna_values(self):
for ambig_char, values in sorted(ambiguous_rna_values.items()):
# Will default to DNA if neither T nor U found...
compl_values = str(Seq.Seq(values).complement().transcribe())
ambig_values = ambiguous_rna_values[
ambiguous_rna_complement[ambig_char]]
self.assertEqual(set(compl_values), set(ambig_values))
def test_complement_ambiguous_rna_values(self):
for ambig_char, values in sorted(ambiguous_rna_values.items()):
compl_values = str(
Seq.Seq(values, alphabet=IUPAC.ambiguous_rna).complement())
self.assertEqual(
set(compl_values),
set(ambiguous_rna_values[
ambiguous_rna_complement[ambig_char]]))
def test_complement_ambiguous_rna_values(self):
for ambig_char, values in sorted(ambiguous_rna_values.items()):
compl_values = str(
# Will default to DNA if neither T or U found...
# Turn black code style off
# fmt: off
Seq.Seq(values).complement().transcribe()
# fmt: on
)
ambig_values = ambiguous_rna_values[
ambiguous_rna_complement[ambig_char]]
self.assertEqual(set(compl_values), set(ambig_values))
print("")
print("DNA Ambiguity mapping: %s" % sorted_dict(ambiguous_dna_values))
print("DNA Complement mapping: %s" % sorted_dict(ambiguous_dna_complement))
for ambig_char, values in sorted(ambiguous_dna_values.items()):
compl_values = complement(values)
print("%s={%s} --> {%s}=%s" % (ambig_char, values, compl_values,
ambiguous_dna_complement[ambig_char]))
assert set(compl_values) == set(
ambiguous_dna_values[ambiguous_dna_complement[ambig_char]])
print("")
print("RNA Ambiguity mapping: %s" % sorted_dict(ambiguous_rna_values))
print("RNA Complement mapping: %s" % sorted_dict(ambiguous_rna_complement))
for ambig_char, values in sorted(ambiguous_rna_values.items()):
compl_values = complement(values).replace(
"T", "U") # need to help as no alphabet
print("%s={%s} --> {%s}=%s" % (ambig_char, values, compl_values,
ambiguous_rna_complement[ambig_char]))
assert set(compl_values) == set(
ambiguous_rna_values[ambiguous_rna_complement[ambig_char]])
print("")
print("Reverse complements:")
for sequence in [
Seq.Seq("".join(sorted(ambiguous_rna_values))),
Seq.Seq("".join(sorted(ambiguous_dna_values))),
Seq.Seq("".join(sorted(ambiguous_rna_values)), Alphabet.generic_rna),
Seq.Seq("".join(sorted(ambiguous_dna_values)), Alphabet.generic_dna),
Seq.Seq("".join(sorted(ambiguous_rna_values)).replace("X", ""),
return "{%s}" % ", ".join("%s: %s" % (repr(k), repr(v))
for k, v in sorted(d.items()))
print("")
print("DNA Ambiguity mapping: %s" % sorted_dict(ambiguous_dna_values))
print("DNA Complement mapping: %s" % sorted_dict(ambiguous_dna_complement))
for ambig_char, values in sorted(ambiguous_dna_values.items()):
compl_values = complement(values)
print("%s={%s} --> {%s}=%s" %
(ambig_char, values, compl_values, ambiguous_dna_complement[ambig_char]))
assert set(compl_values) == set(ambiguous_dna_values[ambiguous_dna_complement[ambig_char]])
print("")
print("RNA Ambiguity mapping: %s" % sorted_dict(ambiguous_rna_values))
print("RNA Complement mapping: %s" % sorted_dict(ambiguous_rna_complement))
for ambig_char, values in sorted(ambiguous_rna_values.items()):
compl_values = complement(values).replace("T", "U") # need to help as no alphabet
print("%s={%s} --> {%s}=%s" %
(ambig_char, values, compl_values, ambiguous_rna_complement[ambig_char]))
assert set(compl_values) == set(ambiguous_rna_values[ambiguous_rna_complement[ambig_char]])
print("")
print("Reverse complements:")
for sequence in [Seq.Seq("".join(sorted(ambiguous_rna_values))),
Seq.Seq("".join(sorted(ambiguous_dna_values))),
Seq.Seq("".join(sorted(ambiguous_rna_values)), Alphabet.generic_rna),
Seq.Seq("".join(sorted(ambiguous_dna_values)), Alphabet.generic_dna),
Seq.Seq("".join(sorted(ambiguous_rna_values)).replace("X", ""), IUPAC.IUPACAmbiguousRNA()),
Seq.Seq("".join(sorted(ambiguous_dna_values)).replace("X", ""), IUPAC.IUPACAmbiguousDNA()),
Seq.Seq("AWGAARCKG")]: # Note no U or T
print("%s -> %s"
def test_complement_ambiguous_rna_values(self):
for ambig_char, values in sorted(ambiguous_rna_values.items()):
compl_values = str(Seq.Seq(values, alphabet=IUPAC.ambiguous_rna).complement())
self.assertEqual(set(compl_values),
set(ambiguous_rna_values[ambiguous_rna_complement[ambig_char]]))
