def _get_template_sequence_in_target_range(self, alignment, target_range):
"""
For the given target sequence range, this function returns the
corresponding sequence of the template, according to the given alignment.
"""
target_start = 0
while not is_amino_acid_char(alignment.target_alignment[target_start]):
target_start += 1
start = target_start
n_aa = 0
while n_aa < target_range.start and start < len(
alignment.target_alignment):
if is_amino_acid_char(alignment.target_alignment[start]):
n_aa += 1
start += 1
end = start
n_aa = 0
while n_aa < target_range.get_length() and end < len(
alignment.target_alignment):
if is_amino_acid_char(alignment.target_alignment[end]):
n_aa += 1
end += 1
return alignment.template_alignment[start:end]
def count_aligned_residues(self, id1, id2):
nalign = 0
for i in range(len(self.aligned_sequences[id1])):
if is_amino_acid_char(self.aligned_sequences[id1][i]) and \
is_amino_acid_char(self.aligned_sequences[id2][i]):
nalign += 1
return nalign
def _get_template_sequence_in_target_range(self, alignment, target_range):
"""
For the given target sequence range, this function returns the
corresponding sequence of the template, according to the given alignment.
"""
target_start = 0
while not is_amino_acid_char(alignment.target_alignment[target_start]):
target_start += 1
start = target_start
n_aa = 0
while n_aa < target_range.start and start < len(alignment.target_alignment):
if is_amino_acid_char(alignment.target_alignment[start]):
n_aa += 1
start += 1
end = start
n_aa = 0
while n_aa < target_range.get_length() and end < len(alignment.target_alignment):
if is_amino_acid_char(alignment.target_alignment[end]):
n_aa += 1
end += 1
return alignment.template_alignment[start: end]
def _merge_alignments(self, alignment1, alignment2):
span1 = alignment1.get_relative_span()
span2 = alignment2.get_relative_span()
# make sure span1 is the N-sided:
if span2 < span1:
span1, span2 = swap(span1, span2)
alignment1, alignment2 = swap(alignment1, alignment2)
# Determine alignment positions of span1 and span2:
i1 = 0
naa = 0
while naa < span1.end:
if is_amino_acid_char(alignment1.template_alignment[i1]):
naa += 1
i1 += 1
i2 = 0
naa = 0
while naa < span2.start:
if is_amino_acid_char(alignment2.template_alignment[i2]):
naa += 1
i2 += 1
return TargetTemplateAlignment(alignment1.target_alignment[: i1] + alignment2.target_alignment[i2: ],
alignment1.template_alignment[: i1] + alignment2.template_alignment[i2: ])
def count_aligned_residues(self, id1, id2):
nalign = 0
for i in range(len(self.aligned_sequences[id1])):
if is_amino_acid_char(self.aligned_sequences[id1][i]) and \
is_amino_acid_char(self.aligned_sequences[id2][i]):
nalign += 1
return nalign
def _merge_alignments(self, alignment1, alignment2):
span1 = alignment1.get_relative_span()
span2 = alignment2.get_relative_span()
# make sure span1 is the N-sided:
if span2 < span1:
span1, span2 = swap(span1, span2)
alignment1, alignment2 = swap(alignment1, alignment2)
# Determine alignment positions of span1 and span2:
i1 = 0
naa = 0
while naa < span1.end:
if is_amino_acid_char(alignment1.template_alignment[i1]):
naa += 1
i1 += 1
i2 = 0
naa = 0
while naa < span2.start:
if is_amino_acid_char(alignment2.template_alignment[i2]):
naa += 1
i2 += 1
return TargetTemplateAlignment(alignment1.target_alignment[: i1] + alignment2.target_alignment[i2: ],
alignment1.template_alignment[: i1] + alignment2.template_alignment[i2: ])
def get_covered_template_residues_indices(self):
n = 0
covered = []
for i in range(len(self.aligned_sequences['target'])):
if is_amino_acid_char(self.aligned_sequences['template'][i]):
if is_amino_acid_char(self.aligned_sequences['target'][i]):
covered.append(n)
n += 1
return covered
def get_percentage_coverage(self):
nalign = 0
ntar = 0
for i in range(len(self.aligned_sequences['target'])):
if is_amino_acid_char(self.aligned_sequences['target'][i]):
ntar += 1
if is_amino_acid_char(self.aligned_sequences['template'][i]):
nalign += 1
return (100.0 * nalign) / ntar
def get_percentage_coverage(self):
nalign = 0
nq = 0
for i in range(len(self.aligned_sequences['query'])):
if is_amino_acid_char(self.aligned_sequences['query'][i]):
nq += 1
if is_amino_acid_char(self.aligned_sequences['subject'][i]):
nalign += 1
return (100.0 * nalign) / nq
def get_covered_template_residues_indices(self):
n = 0
covered = []
for i in range(len(self.aligned_sequences['target'])):
if is_amino_acid_char(self.aligned_sequences['template'][i]):
if is_amino_acid_char(self.aligned_sequences['target'][i]):
covered.append(n)
n += 1
return covered
def get_percentage_coverage(self):
nalign = 0
ntar = 0
for i in range(len(self.aligned_sequences['target'])):
if is_amino_acid_char(self.aligned_sequences['target'][i]):
ntar += 1
if is_amino_acid_char(self.aligned_sequences['template'][i]):
nalign += 1
return (100.0 * nalign) / ntar
def get_percentage_coverage(self):
nalign = 0
nq = 0
for i in range(len(self.aligned_sequences['query'])):
if is_amino_acid_char(self.aligned_sequences['query'][i]):
nq += 1
if is_amino_acid_char(self.aligned_sequences['subject'][i]):
nalign += 1
return (100.0 * nalign) / nq
def is_target_residue_covered(self, residue_number):
n = 1
for i in range(len(self.aligned_sequences['target'])):
if is_amino_acid_char(self.aligned_sequences['target'][i]):
if n == residue_number and \
is_amino_acid_char(self.aligned_sequences['template'][i]):
return True
n += 1
return False
def is_target_residue_covered(self, residue_number):
n = 1
for i in range(len(self.aligned_sequences['target'])):
if is_amino_acid_char(self.aligned_sequences['target'][i]):
if n == residue_number and \
is_amino_acid_char(self.aligned_sequences['template'][i]):
return True
n += 1
return False
def is_query_residue_covered(self, residue_number):
n = self.query_start
for i in range(len(self.aligned_sequences['query'])):
if is_amino_acid_char(self.aligned_sequences['query'][i]):
if n == residue_number and \
is_amino_acid_char(self.aligned_sequences['subject'][i]):
return True
n += 1
return False
def is_query_residue_covered(self, residue_number):
n = self.query_start
for i in range(len(self.aligned_sequences['query'])):
if is_amino_acid_char(self.aligned_sequences['query'][i]):
if n == residue_number and \
is_amino_acid_char(self.aligned_sequences['subject'][i]):
return True
n += 1
return False
def get_percentage_identity(self, id1, id2):
nalign = 0
nid = 0
for i in range(len(self.aligned_sequences[id1])):
if is_amino_acid_char(self.aligned_sequences[id1][i]) and \
is_amino_acid_char(self.aligned_sequences[id2][i]):
nalign += 1
if self.aligned_sequences[id1][i] == self.aligned_sequences[id2][i]:
nid += 1
if nalign > 0:
return (100.0 * nid) / nalign
else:
return 0.0
def get_percentage_identity(self, id1, id2):
nalign = 0
nid = 0
for i in range(len(self.aligned_sequences[id1])):
if is_amino_acid_char(self.aligned_sequences[id1][i]) and \
is_amino_acid_char(self.aligned_sequences[id2][i]):
nalign += 1
if self.aligned_sequences[id1][i] == self.aligned_sequences[
id2][i]:
nid += 1
if nalign > 0:
return (100.0 * nid) / nalign
else:
return 0.0
def get_relative_span(self):
"""
Tells the starting position of 'target' relative to
the starting position of 'template'.
"""
i = 0
while not is_amino_acid_char(self.target_alignment[i]):
i += 1
start = len(self.template_alignment[:i].replace('-', ''))
i = len(self.target_alignment)
while not is_amino_acid_char(self.target_alignment[i - 1]):
i -= 1
end = len(self.template_alignment[:i].replace('-', ''))
return SequenceRange(start, end, self.get_template_sequence())
def get_relative_span(self):
"""
Tells the starting position of 'target' relative to
the starting position of 'template'.
"""
i = 0
while not is_amino_acid_char(self.target_alignment[i]):
i += 1
start = len(self.template_alignment[:i].replace('-', ''))
i = len(self.target_alignment)
while not is_amino_acid_char(self.target_alignment[i - 1]):
i -= 1
end = len(self.template_alignment[:i].replace('-', ''))
return SequenceRange(start, end, self.get_template_sequence())