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())