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# Copyright 2003 by Bartek Wilczynski. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Parsing AlignACE output files."""
from Bio.motifs import Motif, Instances
from Bio.Seq import Seq
class Record(list):
"""AlignACE record (subclass of Python list)."""
def __init__(self):
"""Initialize the class."""
self.parameters = None
def read(handle):
"""Parse an AlignACE format handle as a Record object."""
record = Record()
line = next(handle)
record.version = line.strip()
line = next(handle)
record.command = line.strip()
mask = None
number = None
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":
alphabet = "ACGT"
instances = Instances(instances, alphabet)
motif = Motif(alphabet, instances)
motif.score = float(line.split()[-1])
motif.number = number
motif.mask = mask
record.append(motif)
elif len(line.split("\t")) == 4:
seq = Seq(line.split("\t")[0])
instances.append(seq)
elif "*" in line:
mask = line.strip("\r\n")
else:
raise ValueError(line)
return record
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