for row in zip(*dna_strings):
count = Counter(row)
self._matrix.append([
count['A'],
count['C'],
count['G'],
count['T']])
self._consensus = ''
def __str__(self):
return pprint.pformat(list(zip(*self._matrix)))
@property
def consensus(self):
possibles = list('ACGT')
parts = []
for row in self._matrix:
most_common = max(range(len(row)), key=row.__getitem__)
parts.append(possibles[most_common])
return ''.join(parts)
@consensus.setter
def consensus(self, value):
raise TypeError('Profile matrix object does not support assignment.')
with open('data/consensus_and_profile.txt') as fp:
p = ProfileMatrix(parse_fasta(fp).values())
print(p.consensus)
from bioinformatics.genetics import gc_content
from bioinformatics.genetics import parse_fasta
with open('data/computing_gc_content.txt') as file_handle:
dna_strings = parse_fasta(file_handle)
gc_contents = [(id_, gc_content(dna_string))
for id_, dna_string in dna_strings]
print(*sorted(gc_contents, key=lambda x: x[1])[-1], sep='\n')
