def test_distance_dna_google(self):
dist = bbc.Distance(self.vector, 'google')
matrix = distmatrix.create(self.dna_records.id_list, dist)
exp = [
" 3", "seq1 0.0000000 73.1311144 37.1219467",
"seq2 73.1311144 0.0000000 33.2221873",
"seq3 37.1219467 33.2221873 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))
def test_distance_dna_euclidnorm(self):
dist = bbc.Distance(self.vector)
matrix = distmatrix.create(self.dna_records.id_list, dist)
exp = [
" 3", "seq1 0.0000000 1.0227476 1.9351116",
"seq2 1.0227476 0.0000000 1.4469591",
"seq3 1.9351116 1.4469591 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))
def test_distance_pep_google(self):
vector = bbc.create_vectors(self.pep_records, 10, utils.ALPHABET_PEP)
dist = bbc.Distance(vector, 'google')
matrix = distmatrix.create(self.pep_records.id_list, dist)
exp = [
" 4", "seq1 0.0000000 862.9400129 912.1886801 233.2058119",
"seq2 862.9400129 0.0000000 694.9729647 237.9720958",
"seq3 912.1886801 694.9729647 0.0000000 225.2262758",
"seq4 233.2058119 237.9720958 225.2262758 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))
def main():
parser = get_parser()
args = validate_args(parser)
seq_records = seqrecords.read_fasta(args.fasta)
vector = bbc.create_vectors(seq_records, args.k, alphabet=args.alphabet)
dist = bbc.Distance(vector)
matrix = distmatrix.create(seq_records.id_list, dist)
if args.out:
oh = open(args.out, 'w')
matrix.write_to_file(oh, args.outfmt)
oh.close()
else:
matrix.display(args.outfmt)
sys.stderr.write("Too many arguments\n")
exit(1)
else:
method = sys.argv[1]
infile = sys.argv[2]
outfile = sys.argv[3]
input_file = open(infile, 'r')
seq_records = seqrecords.read_fasta(input_file)
input_file.close()
#choose one method to compute distance matrix
if method == "bbc":
alphabet = seqcontent.get_alphabet('protein')
vector = bbc.create_vectors(seq_records, 10, alphabet)
dist = bbc.Distance(vector)
matrix = distmatrix.create(seq_records.id_list, dist)
matrix.display()
elif method == "ncd":
dist = ncd.Distance(seq_records)
matrix = distmatrix.create(seq_records.id_list, dist)
matrix.display()
elif method == "wmetric":
matrix = subsmat.get('blosum62')
dist = wmetric.Distance(seq_records, matrix)
matrix = distmatrix.create(seq_records.id_list, dist)
matrix.display()
elif method == "d2":