def _initIUPAC(self,consensus):
"""Sets Motif's attributes using an IUPAC motif string."""
IUPAC.__init__(self,consensus)
def _motil2myMat():
"""Convert motility's matrix data to my format and
return the PWM/barcode."""
pwm = {}
bases = sorted(self.bases)
for i in range(4):
baseData = []
for pos in self.matrix:
baseData.append(pos[i])
pwm[bases[i]] = tuple(baseData)
bc = hashlib.md5(str(pwm)).hexdigest()
return pwm,bc
self.consensus = self.motif
self.pwm,self.barcode = _motil2myMat()
self._setID()
self.accession = self.id
def test_mismatches(self):
motif = 'WGATAR'
motif_obj = IUPAC(motif)
assert len(motif_obj.find_with_mismatches('NGATAN', 0)) == 0
assert len(motif_obj.find_with_mismatches('NGATAN', 1)) == 0
assert len(motif_obj.find_with_mismatches('NGATAN', 2)) == 1
assert len(motif_obj.find_with_mismatches('NGATAN', 3)) == 1
assert len(motif_obj.find_with_mismatches('NGATAN',
4)) == 2 # finds RC
try:
motif_obj.find_with_mismatches('NGATAN', 6)
assert 0
except Exception, e:
pass
def test_mismatches(self):
motif = 'WGATAR'
motif_obj = IUPAC(motif)
assert len(motif_obj.find_with_mismatches('NGATAN', 0)) == 0
assert len(motif_obj.find_with_mismatches('NGATAN', 1)) == 0
assert len(motif_obj.find_with_mismatches('NGATAN', 2)) == 1
assert len(motif_obj.find_with_mismatches('NGATAN', 3)) == 1
assert len(motif_obj.find_with_mismatches('NGATAN', 4)) == 2 # finds RC
try:
motif_obj.find_with_mismatches('NGATAN', 6)
assert 0
except Exception, e:
pass
def test_g(self):
motif = 'G'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 0
assert len(motif_obj.find('A')) == 0
assert motif_obj.calc_score('A') == 0
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 0 # DOES NOT do RC
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 0
assert len(motif_obj.find('T')) == 0
assert motif_obj.calc_score('T') == 0
assert len(find_iupac('N', motif)) == 0
assert len(motif_obj.find('N')) == 0
assert motif_obj.calc_score('N') == 0
def test_min(self):
for motif in self.misc_motifs:
motif_obj = IUPAC(motif)
assert motif_obj.min_score() == motif.count('N')
def test_max(self):
for motif in self.misc_motifs:
motif_obj = IUPAC(motif)
assert motif_obj.max_score() == len(motif)
def test_n(self):
motif = 'N'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 1
assert len(motif_obj.find('A')) == 1
assert motif_obj.calc_score('A') == 1
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 1
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 1
assert len(motif_obj.find('T')) == 1
assert motif_obj.calc_score('T') == 1
assert len(find_iupac('N', motif)) == 1
assert len(motif_obj.find('N')) == 1
assert motif_obj.calc_score('N') == 1
def test_g(self):
motif = 'G'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 0
assert len(motif_obj.find('A')) == 0
assert motif_obj.calc_score('A') == 0
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 0 # DOES NOT do RC
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 0
assert len(motif_obj.find('T')) == 0
assert motif_obj.calc_score('T') == 0
assert len(find_iupac('N', motif)) == 0
assert len(motif_obj.find('N')) == 0
assert motif_obj.calc_score('N') == 0
def test_min(self):
for motif in self.misc_motifs:
motif_obj = IUPAC(motif)
assert motif_obj.min_score() == motif.count('N')
def test_max(self):
for motif in self.misc_motifs:
motif_obj = IUPAC(motif)
assert motif_obj.max_score() == len(motif)
def test_n(self):
motif = 'N'
motif_obj = IUPAC(motif)
assert len(find_iupac('A', motif)) == 1
assert len(motif_obj.find('A')) == 1
assert motif_obj.calc_score('A') == 1
assert len(find_iupac('C', motif)) == 1
assert len(motif_obj.find('C')) == 1
assert motif_obj.calc_score('C') == 1
assert len(find_iupac('G', motif)) == 1
assert len(motif_obj.find('G')) == 1
assert motif_obj.calc_score('G') == 1
assert len(find_iupac('T', motif)) == 1
assert len(motif_obj.find('T')) == 1
assert motif_obj.calc_score('T') == 1
assert len(find_iupac('N', motif)) == 1
assert len(motif_obj.find('N')) == 1
assert motif_obj.calc_score('N') == 1
def test_len(self):
for motif in self.misc_motifs:
motif_obj = IUPAC(motif)
assert len(motif_obj) == len(motif)