""" Classes for reading and writing motif data. """ from bx.motif.pwm import FrequencyMatrix class TransfacMotif: def __init__(self): self.accession = None self.id = None self.dates = None self.name = None self.description = None self.binding_factors = None self.basis = None self.comment = None self.matrix = None self.attributes = None self.sites = None transfac_actions = { "AC": ("store_single", "accession"), "ID": ("store_single", "id"), "DT": ("store_single_list", "dates"), "NA": ("store_single", "name"), "DE": ("store_block", "description"), "BF": ("store_single_list", "binding_factors"), "BA": ("store_block", "basis"), "CC": ("store_block", "comment"), "P0": ("store_matrix", "matrix"), # For CREAD format files "TY": ("store_single", "type"), "AT": ("store_single_key_value", "attributes"), "BS": ("store_single_list", "sites"), } class TransfacReader: """ Reads motifs in TRANSFAC format. """ parse_actions = transfac_actions def __init__(self, input): self.input = iter(input) self.input_exhausted = False def as_dict(self, key="id"): """ Return a dictionary containing all remaining motifs, using `key` as the dictionary key. """ rval = {} for motif in self: rval[getattr(motif, key)] = motif return rval def __iter__(self): return self def __next__(self): rval = self.next_motif() while rval is None: rval = self.next_motif() return rval def next_motif(self): if self.input_exhausted: raise StopIteration # Accumulate lines until either the end of record indicator "//" is # encounted or the input is exhausted. lines = [] while True: try: line = next(self.input) except StopIteration: self.input_exhausted = True break if line.startswith("//"): break if not line.isspace(): lines.append(line) if lines: return self.parse_record(lines) def parse_record(self, lines): """ Parse a TRANSFAC record out of `lines` and return a motif. """ # Break lines up temp_lines = [] for line in lines: fields = line.rstrip("\r\n").split(None, 1) if len(fields) == 1: fields.append("") temp_lines.append(fields) lines = temp_lines # Fill in motif from lines motif = TransfacMotif() current_line = 0 while True: # Done parsing if no more lines to consume if current_line >= len(lines): break # Remove prefix and first separator from line prefix, rest = lines[current_line] # No action for this prefix, just ignore the line if prefix not in self.parse_actions: current_line += 1 continue # Get action for line action = self.parse_actions[prefix] # Store a single line value if action[0] == "store_single": key = action[1] setattr(motif, key, rest) current_line += 1 # Add a single line value to a list if action[0] == "store_single_list": key = action[1] if not getattr(motif, key): setattr(motif, key, []) getattr(motif, key).append(rest) current_line += 1 # Add a single line value to a dictionary if action[0] == "store_single_key_value": key = action[1] k, v = rest.strip().split("=", 1) if not getattr(motif, key): setattr(motif, key, {}) getattr(motif, key)[k] = v current_line += 1 # Store a block of text if action[0] == "store_block": key = action[1] value = [] while current_line < len(lines) and lines[current_line][0] == prefix: value.append(lines[current_line][1]) current_line += 1 setattr(motif, key, str.join("\n", value)) # Store a matrix if action[0] == "store_matrix": # First line is alphabet alphabet = rest.split() alphabet_size = len(alphabet) rows = [] pattern = "" current_line += 1 # Next lines are the rows of the matrix (we allow 0 rows) while current_line < len(lines): prefix, rest = lines[current_line] # Prefix should be a two digit 0 padded row number if not prefix.isdigit(): break # The first `alphabet_size` fields are the row values values = rest.split() rows.append([float(_) for _ in values[:alphabet_size]]) # TRANSFAC includes an extra column with the IUPAC code if len(values) > alphabet_size: pattern += values[alphabet_size] current_line += 1 # Only store the pattern if it is the correct length (meaning # that every row had an extra field) if len(pattern) != len(rows): pattern = None matrix = FrequencyMatrix.from_rows(alphabet, rows) setattr(motif, action[1], matrix) # Only return a motif if we saw at least ID or AC or NA if motif.id or motif.accession or motif.name: return motif class TransfacWriter: """ Writes motifs in TRANSFAC format. """ actions = transfac_actions def __init__(self, output): self.output = output def write(self, motif): output = self.output for prefix, actions in self.actions.items(): action = actions[0] if action == "store_single": key = actions[1] if getattr(motif, key) is not None: print(prefix, " ", getattr(motif, key), file=output) print("XX", file=output) elif action == "store_single_list": key = actions[1] if getattr(motif, key) is not None: value = getattr(motif, key) for v in value: print(prefix, " ", v, file=output) print("XX", file=output) elif action == "store_single_key_value": key = actions[1] if getattr(motif, key) is not None: value = getattr(motif, key) for k, v in value.items(): print(prefix, " ", f"{k}={v}", file=output) print("XX", file=output) elif action == "store_block": key = actions[1] if getattr(motif, key) is not None: value = getattr(motif, key) for line in value.split("\n"): print(prefix, " ", line, file=output) print("XX", file=output) elif action == "store_matrix": key = actions[1] if getattr(motif, key) is not None: matrix = getattr(motif, key) print(prefix, " ", " ".join(s.rjust(6) for s in matrix.alphabet), file=output) for i in range(matrix.width): print( "%02d" % (i + 1), " ", " ".join( str(matrix.values[i, matrix.char_to_index[ord(s)]]).rjust(6) for s in matrix.alphabet ), file=output, ) print("XX", file=output) print("//")