def read(handle): """read(handle)""" record = Record() line = handle.next() record.version = line.strip() line = handle.next() record.command = line.strip() for line in handle: line = line.strip() if line == "": pass elif line[:4] == "Para": record.parameters = {} elif line[0] == "#": seq_name = line.split("\t")[1] record.sequences.append(seq_name) elif "=" in line: par_name, par_value = line.split("=") par_name = par_name.strip() par_value = par_value.strip() record.parameters[par_name] = par_value elif line[:5] == "Input": record.sequences = [] elif line[:5] == "Motif": words = line.split() assert words[0] == "Motif" number = int(words[1]) instances = [] elif line[:3] == "MAP": motif = Motif(IUPAC.unambiguous_dna, instances) motif.score = float(line.split()[-1]) motif.number = number motif.set_mask(mask) record.motifs.append(motif) elif len(line.split("\t")) == 4: seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna) instances.append(seq) elif "*" in line: mask = line.strip("\r\n") else: raise ValueError(line) return record
def read(handle): """read(handle)""" record = Record() line = handle.next() record.version = line.strip() line = handle.next() record.command = line.strip() for line in handle: line = line.strip() if line == "": pass elif line[:4] == "Para": record.parameters = {} elif line[0] == "#": seq_name = line.split("\t")[1] record.sequences.append(seq_name) elif "=" in line: par_name, par_value = line.split("=") par_name = par_name.strip() par_value = par_value.strip() record.parameters[par_name] = par_value elif line[:5] == "Input": record.sequences = [] elif line[:5] == "Motif": current_motif = Motif() current_motif.alphabet = IUPAC.unambiguous_dna record.motifs.append(current_motif) elif line[:3] == "MAP": current_motif.score = float(line.split()[-1]) elif len(line.split("\t")) == 4: seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna) current_motif.add_instance(seq) elif "*" in line: current_motif.set_mask(line.strip("\n\c")) else: raise ValueError(line) return record
def read(handle): """read(handle)""" record = Record() line = handle.next() record.version = line.strip() line = handle.next() record.command = line.strip() for line in handle: line = line.strip() if line=="": pass elif line[:4]=="Para": record.parameters={} elif line[0]=="#": seq_name = line.split("\t")[1] record.sequences.append(seq_name) elif "=" in line: par_name, par_value = line.split("=") par_name = par_name.strip() par_value = par_value.strip() record.parameters[par_name]=par_value elif line[:5]=="Input": record.sequences=[] elif line[:5]=="Motif": current_motif = Motif() current_motif.alphabet=IUPAC.unambiguous_dna record.motifs.append(current_motif) elif line[:3]=="MAP": current_motif.score = float(line.split()[-1]) elif len(line.split("\t"))==4: seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna) current_motif.add_instance(seq) elif "*" in line: current_motif.set_mask(line.strip("\n\c")) else: raise ValueError(line) return record