def _aligned_number(self, aln: MultipleSeqAlignment):
return len([
i for i in range(aln.get_alignment_length())
if '-' not in aln[:, i]
])
class PolymorphismSampler(object):
"""docstring for PolymorphismSampler"""
def __init__(self):
super(PolymorphismSampler, self).__init__()
self.sequences = None
self.alignment = None
self.polymorphisms = dict()
self.subsampled = set()
self.num_positions = []
self.num_polymorphisms = []
def read_sequences(self, handle):
sequences = [s for s in SeqIO.parse(handle, 'fasta')]
counts = Counter([len(s) for s in sequences])
mc_length = counts.most_common(1)[0][0]
filtered_sequences = list()
for s in sequences:
if len(s.seq) == mc_length:
filtered_sequences.append(s)
self.sequences = filtered_sequences
def identify_polymorphisms(self):
self.alignment = MultipleSeqAlignment(self.sequences)
for col in range(self.alignment.get_alignment_length()):
polmorphs = set(self.alignment[:,col])
if len(polmorphs) > 1:
self.polymorphisms[col] = polmorphs
def number_of_polymorphisms(self):
total_polymorphisms = 0
for pos, polymorphs in self.polymorphisms.items():
total_polymorphisms += len(polymorphs)
return total_polymorphisms
def subsample(self):
while len(self.polymorphisms.keys()) > 0:
try:
# Choose a seqrecord at random, based on LH sampling criteria.
pos = choice(list(self.polymorphisms.keys()))
letter = choice(list(self.polymorphisms[pos]))
filtered = MultipleSeqAlignment([s for s in self.alignment if s[pos] == letter])
seqrecord = choice(filtered)
self.subsampled.add(seqrecord)
# Remove polymorphisms
for pos in self.polymorphisms.keys():
if seqrecord.seq[pos] in self.polymorphisms[pos]:
self.polymorphisms[pos].remove(seqrecord.seq[pos])
# Update data
self.polymorphisms = {k:v for k,v in self.polymorphisms.items() if len(v) > 0}
self.num_polymorphisms.append(self.number_of_polymorphisms())
self.num_positions.append(len(self.polymorphisms.keys()))
except IndexError:
break
