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# Copyright 2009 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.
"""Unittests for the Seq objects."""
import unittest
from string import maketrans
from Bio.Alphabet import generic_protein, generic_nucleotide, \
generic_dna, generic_rna
from Bio.Alphabet.IUPAC import protein, extended_protein
from Bio.Alphabet.IUPAC import unambiguous_dna, ambiguous_dna, ambiguous_rna
from Bio.Data.IUPACData import ambiguous_dna_values, ambiguous_rna_values
from Bio.Seq import Seq, UnknownSeq, MutableSeq
from Bio.Data.CodonTable import TranslationError
class StringMethodTests(unittest.TestCase):
_examples = [ \
Seq("ACGTGGGGT", generic_protein),
Seq("ACGTGGGGT", generic_nucleotide),
Seq("ACGTGGGGT", generic_dna),
Seq("ACGUGGGGU", generic_rna),
Seq("GG", generic_protein),
Seq("GG", generic_nucleotide),
Seq("GG", generic_dna),
Seq("GG", generic_rna),
Seq("A", generic_protein),
Seq("A", generic_nucleotide),
Seq("A", generic_dna),
Seq("A", generic_rna),
UnknownSeq(1),
UnknownSeq(1, character="n"),
UnknownSeq(1, generic_rna),
UnknownSeq(1, generic_rna, "n"),
UnknownSeq(1, generic_rna, "N"),
UnknownSeq(10, generic_rna, "N"),
UnknownSeq(10, generic_dna, "N"),
UnknownSeq(10, generic_nucleotide, "N"),
UnknownSeq(10, generic_protein, "X"),
UnknownSeq(10, character="X"),
UnknownSeq(10),
]
for seq in _examples[:]:
if isinstance(seq, Seq):
_examples.append(seq.tomutable())
_start_end_values = [0, 1, 2, 1000, -1, -2, -999]
def _test_method(self, method_name, pre_comp_function=None, start_end=False):
"""Check this method matches the plain string's method."""
assert isinstance(method_name, str)
for example1 in self._examples:
if not hasattr(example1, method_name):
#e.g. MutableSeq does not support find
continue
str1 = str(example1)
for example2 in self._examples:
if not hasattr(example2, method_name):
#e.g. MutableSeq does not support find
continue
str2 = str(example2)
i = getattr(example1,method_name)(str2)
j = getattr(str1,method_name)(str2)
if pre_comp_function:
i = pre_comp_function(i)
j = pre_comp_function(j)
if i != j:
raise ValueError("%s.%s(%s) = %i, not %i" \
% (repr(example1),
method_name,
repr(str2),
i,
j))
try:
i = getattr(example1,method_name)(example2)
j = getattr(str1,method_name)(str2)
if pre_comp_function:
i = pre_comp_function(i)
j = pre_comp_function(j)
if i != j:
raise ValueError("%s.%s(%s) = %i, not %i" \
% (repr(example1),
method_name,
repr(example2),
i,
j))
except TypeError:
#TODO - Check the alphabets do clash!
pass
if start_end:
for start in self._start_end_values:
i = getattr(example1,method_name)(str2, start)
j = getattr(str1,method_name)(str2, start)
if pre_comp_function:
i = pre_comp_function(i)
j = pre_comp_function(j)
if i != j:
raise ValueError("%s.%s(%s, %i) = %i, not %i" \
% (repr(example1),
method_name,
repr(str2),
start,
i,
j))
for end in self._start_end_values:
i = getattr(example1,method_name)(str2, start, end)
j = getattr(str1,method_name)(str2, start, end)
if pre_comp_function:
i = pre_comp_function(i)
j = pre_comp_function(j)
if i != j:
raise ValueError("%s.%s(%s, %i, %i) = %i, not %i" \
% (repr(example1),
method_name,
repr(str2),
start,
end,
i,
j))
def test_str_count(self):
"""Check matches the python string count method."""
self._test_method("count", start_end=True)
def test_str_find(self):
"""Check matches the python string find method."""
self._test_method("find", start_end=True)
def test_str_rfind(self):
"""Check matches the python string rfind method."""
self._test_method("rfind", start_end=True)
def test_str_startswith(self):
"""Check matches the python string startswith method."""
self._test_method("startswith", start_end=True)
try:
self.assert_("ABCDE".startswith(("ABE","OBE","ABC")))
except TypeError:
#Base string only supports this on Python 2.5+, skip this
return
#Now check with a tuple of sub sequences
for example1 in self._examples:
if not hasattr(example1, "startswith"):
#e.g. MutableSeq does not support this
continue
subs = tuple([example1[start:start+2] for start \
in range(0, len(example1)-2,3)])
subs_str = tuple([str(s) for s in subs])
self.assertEqual(str(example1).startswith(subs_str),
example1.startswith(subs))
self.assertEqual(str(example1).startswith(subs_str),
example1.startswith(subs_str)) #strings!
self.assertEqual(str(example1).startswith(subs_str,3),
example1.startswith(subs,3))
self.assertEqual(str(example1).startswith(subs_str,2,6),
example1.startswith(subs,2,6))
def test_str_endswith(self):
"""Check matches the python string endswith method."""
self._test_method("endswith", start_end=True)
try:
self.assert_("ABCDE".endswith(("ABE","OBE","CDE")))
except TypeError:
#Base string only supports this on Python 2.5+, skip this
return
#Now check with a tuple of sub sequences
for example1 in self._examples:
if not hasattr(example1, "endswith"):
#e.g. MutableSeq does not support this
continue
subs = tuple([example1[start:start+2] for start \
in range(0, len(example1)-2,3)])
subs_str = tuple([str(s) for s in subs])
self.assertEqual(str(example1).endswith(subs_str),
example1.endswith(subs))
self.assertEqual(str(example1).startswith(subs_str),
example1.startswith(subs_str)) #strings!
self.assertEqual(str(example1).endswith(subs_str,3),
example1.endswith(subs,3))
self.assertEqual(str(example1).endswith(subs_str,2,6),
example1.endswith(subs,2,6))
def test_str_strip(self):
"""Check matches the python string strip method."""
self._test_method("strip", pre_comp_function=str)
def test_str_rstrip(self):
"""Check matches the python string rstrip method."""
self._test_method("rstrip", pre_comp_function=str)
def test_str_split(self):
"""Check matches the python string rstrip method."""
#Calling (r)split should return a list of Seq-like objects, we'll
#just apply str() to each of them so it matches the string method
self._test_method("rstrip", pre_comp_function=lambda x : map(str,x))
def test_str_rsplit(self):
"""Check matches the python string rstrip method."""
#Calling (r)split should return a list of Seq-like objects, we'll
#just apply str() to each of them so it matches the string method
self._test_method("rstrip", pre_comp_function=lambda x : map(str,x))
def test_str_lsplit(self):
"""Check matches the python string rstrip method."""
#Calling (r)split should return a list of Seq-like objects, we'll
#just apply str() to each of them so it matches the string method
self._test_method("rstrip", pre_comp_function=lambda x : map(str,x))
def test_str_length(self):
"""Check matches the python string __len__ method."""
for example1 in self._examples:
str1 = str(example1)
self.assertEqual(len(example1), len(str1))
def test_str_upper(self):
"""Check matches the python string upper method."""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
str1 = str(example1)
self.assertEqual(str(example1.upper()), str1.upper())
def test_str_upper(self):
"""Check matches the python string lower method."""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
str1 = str(example1)
self.assertEqual(str(example1.lower()), str1.lower())
def test_str_getitem(self):
"""Check slicing and indexing works like a string."""
for example1 in self._examples:
str1 = str(example1)
for i in self._start_end_values:
if abs(i) < len(example1):
self.assertEqual(str(example1[i]), str1[i])
self.assertEqual(str(example1[:i]), str1[:i])
self.assertEqual(str(example1[i:]), str1[i:])
for j in self._start_end_values:
self.assertEqual(str(example1[i:j]), str1[i:j])
for step in range(-3,4):
if step == 0:
try:
print example1[i:j:step]
self._assert(False) #Should fail!
except ValueError:
pass
else:
self.assertEqual(str(example1[i:j:step]), \
str1[i:j:step])
def test_tostring(self):
"""Check str(obj) and obj.tostring() match.
Also check the obj.data attribute for non-MutableSeq objects."""
for example1 in self._examples:
str1 = str(example1)
self.assertEqual(example1.tostring(), str1)
if not isinstance(example1, MutableSeq):
self.assertEqual(example1.data, str1)
def test_tomutable(self):
"""Check obj.tomutable() method."""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
mut = example1.tomutable()
self.assert_(isinstance(mut, MutableSeq))
self.assertEqual(str(mut), str(example1))
self.assertEqual(mut.alphabet, example1.alphabet)
def test_toseq(self):
"""Check obj.toseq() method."""
for example1 in self._examples:
try :
seq = example1.toseq()
except AttributeError :
self.assert_(isinstance(example1, Seq))
continue
self.assert_(isinstance(seq, Seq))
self.assertEqual(str(seq), str(example1))
self.assertEqual(seq.alphabet, example1.alphabet)
def test_the_complement(self):
"""Check obj.complement() method."""
mapping = ""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
try :
comp = example1.complement()
except ValueError, e:
self.assertEqual(str(e), "Proteins do not have complements!")
continue
str1 = str(example1)
#This only does the unambiguous cases
if "U" in str1 or "u" in str1 \
or example1.alphabet==generic_rna:
mapping = maketrans("ACGUacgu","UGCAugca")
elif "T" in str1 or "t" in str1 \
or example1.alphabet==generic_dna \
or example1.alphabet==generic_nucleotide:
mapping = maketrans("ACGTacgt","TGCAtgca")
elif "A" not in str1 and "a" not in str1:
mapping = maketrans("CGcg","GCgc")
else :
#TODO - look at alphabet?
assert False, example1
continue
self.assertEqual(str1.translate(mapping), str(comp))
self.assertEqual(comp.alphabet, example1.alphabet)
def test_the_reverse_complement(self):
"""Check obj.reverse_complement() method."""
mapping = ""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
try :
comp = example1.reverse_complement()
except ValueError, e:
self.assertEqual(str(e), "Proteins do not have complements!")
continue
str1 = str(example1)
#This only does the unambiguous cases
if "U" in str1 or "u" in str1 \
or example1.alphabet==generic_rna:
mapping = maketrans("ACGUacgu","UGCAugca")
elif "T" in str1 or "t" in str1 \
or example1.alphabet==generic_dna \
or example1.alphabet==generic_nucleotide:
mapping = maketrans("ACGTacgt","TGCAtgca")
elif "A" not in str1 and "a" not in str1:
mapping = maketrans("CGcg","GCgc")
else :
#TODO - look at alphabet?
continue
self.assertEqual(str1.translate(mapping)[::-1], str(comp))
self.assertEqual(comp.alphabet, example1.alphabet)
def test_the_transcription(self):
"""Check obj.transcribe() method."""
mapping = ""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
try :
tran = example1.transcribe()
except ValueError, e:
if str(e) == "Proteins cannot be transcribed!" : continue
if str(e) == "RNA cannot be transcribed!" : continue
raise e
str1 = str(example1)
self.assertEqual(str1.replace("T","U").replace("t","u"), str(tran))
self.assertEqual(tran.alphabet, generic_rna) #based on limited examples
def test_the_back_transcription(self):
"""Check obj.back_transcribe() method."""
mapping = ""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
try :
tran = example1.back_transcribe()
except ValueError, e:
if str(e) == "Proteins cannot be back transcribed!" : continue
if str(e) == "DNA cannot be back transcribed!" : continue
raise e
str1 = str(example1)
self.assertEqual(str1.replace("U","T").replace("u","t"), str(tran))
self.assertEqual(tran.alphabet, generic_dna) #based on limited examples
def test_the_translate(self):
"""Check obj.translate() method."""
mapping = ""
for example1 in self._examples:
if isinstance(example1, MutableSeq) : continue
try :
tran = example1.translate()
except ValueError, e:
if str(e) == "Proteins cannot be translated!" : continue
raise e
#This is based on the limited example not having stop codons:
if tran.alphabet not in [extended_protein, protein, generic_protein]:
print tran.alphabet
self.assert_(False)
#TODO - check the actual translation, and all the optional args
def test_the_translation_of_stops(self):
"""Check obj.translate() method with stop codons."""
misc_stops = "TAATAGTGAAGAAGG"
for nuc in [Seq(misc_stops),
Seq(misc_stops, generic_nucleotide),
Seq(misc_stops, generic_dna),
Seq(misc_stops, unambiguous_dna)]:
self.assertEqual("***RR", str(nuc.translate()))
self.assertEqual("***RR", str(nuc.translate(1)))
self.assertEqual("***RR", str(nuc.translate("SGC0")))
self.assertEqual("**W**", str(nuc.translate(table=2)))
self.assertEqual("**WRR", str(nuc.translate(table='Yeast Mitochondrial')))
self.assertEqual("**WSS", str(nuc.translate(table=5)))
self.assertEqual("**WSS", str(nuc.translate(table=9)))
self.assertEqual("**CRR", str(nuc.translate(table='Euplotid Nuclear')))
self.assertEqual("***RR", str(nuc.translate(table=11)))
self.assertEqual("***RR", str(nuc.translate(table='Bacterial')))
self.assertEqual("", str(nuc.translate(to_stop=True)))
self.assertEqual(str(Seq("TAT").translate()), "Y")
self.assertEqual(str(Seq("TAR").translate()), "*")
self.assertEqual(str(Seq("TAN").translate()), "X")
self.assertEqual(str(Seq("NNN").translate()), "X")
self.assertEqual(str(Seq("TAt").translate()), "Y")
self.assertEqual(str(Seq("TaR").translate()), "*")
self.assertEqual(str(Seq("TaN").translate()), "X")
self.assertEqual(str(Seq("nnN").translate()), "X")
self.assertEqual(str(Seq("tat").translate()), "Y")
self.assertEqual(str(Seq("tar").translate()), "*")
self.assertEqual(str(Seq("tan").translate()), "X")
self.assertEqual(str(Seq("nnn").translate()), "X")
def test_the_translation_of_invalid_codons(self):
"""Check obj.translate() method with invalid codons."""
for codon in ["TA?", "N-N", "AC_", "Ac_"]:
for nuc in [Seq(codon),
Seq(codon, generic_nucleotide),
Seq(codon, generic_dna),
Seq(codon, unambiguous_dna)]:
try :
print nuc.translate()
self.assert_(False, "Transating %s should fail" % codon)
except TranslationError :
pass
def test_the_translation_of_ambig_codons(self):
"""Check obj.translate() method with ambiguous codons."""
for letters, ambig_values in [(ambiguous_dna.letters, ambiguous_dna_values),
(ambiguous_rna.letters, ambiguous_rna_values)] :
ambig = set(letters)
for c1 in ambig:
for c2 in ambig:
for c3 in ambig:
values = set([str(Seq(a+b+c).translate()) \
for a in ambig_values[c1] \
for b in ambig_values[c2] \
for c in ambig_values[c3]])
t = str(Seq(c1+c2+c3).translate())
if t=="*":
self.assertEqual(values, set("*"))
elif t=="X":
self.assert_(len(values) > 1, \
"translate('%s') = '%s' not '%s'" \
% (c1+c2+c3, t, ",".join(values)))
elif t=="Z":
self.assertEqual(values, set("EQ"))
elif t=="B":
self.assertEqual(values, set("DN"))
elif t=="J":
self.assertEqual(values, set("LI"))
else:
self.assertEqual(values, set(t))
#TODO - Use the Bio.Data.IUPACData module for the
#ambiguous protein mappings?
#TODO - Addition...
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
|
