def main():
parser = get_parser()
args = validate_args(parser)
seq_records = seqrecords.read_fasta(args.fasta)
if args.word_size:
p = word_pattern.create(seq_records.seq_list, args.word_size)
else:
p = word_pattern.read(args.word_pattern)
if args.reduce_alphabet:
p = p.reduce_alphabet(seqcontent.get_reduced_alphabet(args.molecule))
if args.merge_revcomp:
p = p.merge_revcomp()
freqs = word_vector.Freqs(seq_records.length_list, p)
dist = word_distance.Distance(freqs, args.distance)
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)
def test_distance_hamming(self):
dist = word_sets_distance.Distance(self.pep_records, 2, 'hamming')
matrix = distmatrix.create(self.pep_records.id_list, dist)
exp = [
" 4", "seq1 0 22 44 37", "seq2 22 0 26 31",
"seq3 44 26 0 29", "seq4 37 31 29 0"
]
self.assertEqual(matrix.format(0), "\n".join(exp))
def test_kld_freqs(self):
dist = word_distance.Distance(self.freqs, 'kld')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 0.0932800 0.0435210",
"seq2 0.0932800 0.0000000 0.0447391",
"seq3 0.0435210 0.0447391 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_manhattan_freqs(self):
dist = word_distance.Distance(self.freqs, 'manhattan')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 1.2156863 0.7619048",
"seq2 1.2156863 0.0000000 0.7899160",
"seq3 0.7619048 0.7899160 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_canberra_freqs(self):
dist = word_distance.Distance(self.freqs, 'canberra')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 10.3372258 7.1836838",
"seq2 10.3372258 0.0000000 6.6280959",
"seq3 7.1836838 6.6280959 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
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_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_lcc_freqs(self):
dist = word_distance.Distance(self.freqs, 'lcc')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 0.6205496 0.4017554",
"seq2 0.6205496 0.0000000 0.2550506",
"seq3 0.4017554 0.2550506 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_braycurtis_freqs(self):
dist = word_distance.Distance(self.freqs, 'braycurtis')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 0.6078431 0.3809524",
"seq2 0.6078431 0.0000000 0.3949580",
"seq3 0.3809524 0.3949580 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_diff_abs_mult_freqs(self):
dist = word_distance.Distance(self.freqs, 'diff_abs_mult')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 0.0621975 0.0404611",
"seq2 0.0621975 0.0000000 0.0531478",
"seq3 0.0404611 0.0531478 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_jsd_freqs(self):
dist = word_distance.Distance(self.freqs, 'jsd')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 0.4608882 0.2550278",
"seq2 0.4608882 0.0000000 0.2457790",
"seq3 0.2550278 0.2457790 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_chebyshev_freqs(self):
dist = word_distance.Distance(self.freqs, 'chebyshev')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 0.1936275 0.1250000",
"seq2 0.1936275 0.0000000 0.1428571",
"seq3 0.1250000 0.1428571 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_google_freqs(self):
dist = word_distance.Distance(self.freqs, 'google')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.6078431 0.3809524',
'seq2 0.6078431 0.0000000 0.3949580',
'seq3 0.3809524 0.3949580 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_minkowski_freqs(self):
dist = word_distance.Distance(self.freqs, 'minkowski')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
" 3", "seq1 0.0000000 0.3763512 0.2532387",
"seq2 0.3763512 0.0000000 0.2603008",
"seq3 0.2532387 0.2603008 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_distance1(self):
vecs = fcgr.create_vectors(self.dna_records, 2)
dist = fcgr.Distance(vecs)
matrix = distmatrix.create(self.dna_records.id_list, dist)
exp = [
" 3", "seq1 0.0000000 7.5498344 5.7445626",
"seq2 7.5498344 0.0000000 4.2426407",
"seq3 5.7445626 4.2426407 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))
def test_distance_d(self):
matrix = distmatrix.create(self.pep_records.id_list, self.dist)
exp = [
" 4",
"seq1 0 9 15 20",
"seq2 9 0 10 18",
"seq3 15 10 0 17",
"seq4 20 18 17 0"
]
self.assertEqual(matrix.format(decimal_places=0), "\n".join(exp))
def test_distance(self):
dist = ncd.Distance(self.pep_records)
matrix = distmatrix.create(self.pep_records.id_list, dist)
exp = [
" 4", "seq1 0.0000000 0.2698413 0.3809524 0.5238095",
"seq2 0.2698413 0.0000000 0.2950820 0.4666667",
"seq3 0.3809524 0.2950820 0.0000000 0.4754098",
"seq4 0.5238095 0.4666667 0.4754098 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))
def test_euclid_squared_counts(self):
# The result of this method is identical to that from decaf+py.
dist = distance.Distance(self.counts, 'euclid_squared')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 57.0000000 30.0000000',
'seq2 57.0000000 0.0000000 19.0000000',
'seq3 30.0000000 19.0000000 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def calc_distances(seqs):
seq_records = seqrecords.SeqRecords()
for seq in seqs:
seq_records.add(seq.name, "".join(seq.sequence))
dist = ncd.Distance(seq_records)
matrix = distmatrix.create(seq_records.id_list, dist)
return matrix.data
def test_euclid_seqlen2_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.freqs, 'euclid_seqlen2')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.0072101 0.0038263',
'seq2 0.0072101 0.0000000 0.0039866',
'seq3 0.0038263 0.0039866 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_distance2(self):
vecs = fcgr.create_vectors(self.dna_records, 2)
dist = fcgr.Distance(vecs, 'google')
matrix = distmatrix.create(self.dna_records.id_list, dist)
exp = [
" 3", "seq1 0.0000000 0.5833333 0.5416667",
"seq2 0.5833333 0.0000000 0.4210526",
"seq3 0.5416667 0.4210526 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))
def test_diff_abs_add_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.freqs, 'diff_abs_add')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.0810458 0.0507937',
'seq2 0.0810458 0.0000000 0.0526611',
'seq3 0.0507937 0.0526611 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_diff_abs_mult2_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.freqs, 'diff_abs_mult2')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.0621975 0.0404611',
'seq2 0.0621975 0.0000000 0.0531478',
'seq3 0.0404611 0.0531478 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_euclid_norm_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.freqs, 'euclid_norm')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.3763512 0.2532387',
'seq2 0.3763512 0.0000000 0.2603008',
'seq3 0.2532387 0.2603008 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_angle_cos_evol_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.freqs, 'angle_cos_evol')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.3281368 0.1625980',
'seq2 0.3281368 0.0000000 0.1347925',
'seq3 0.1625980 0.1347925 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_euclid_norm_counts(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.counts, 'euclid_norm')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 7.5498344 5.4772256',
'seq2 7.5498344 0.0000000 4.3588989',
'seq3 5.4772256 4.3588989 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_angle_cos_diss_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.freqs, 'angle_cos_diss')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.2797355 0.1500672',
'seq2 0.2797355 0.0000000 0.1261027',
'seq3 0.1500672 0.1261027 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_euclid_squared_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = word_distance.Distance(self.freqs, 'euclid_squared')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.1416402 0.0641298',
'seq2 0.1416402 0.0000000 0.0677565',
'seq3 0.0641298 0.0677565 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_distance_d1_star(self):
self.dist.set_disttype('d1_star')
matrix = distmatrix.create(self.pep_records.id_list, self.dist)
exp = [
" 4",
"seq1 0.0000000 0.3404255 0.5283019 0.5348837",
"seq2 0.3404255 0.0000000 0.4042553 0.5121951",
"seq3 0.5283019 0.4042553 0.0000000 0.5135135",
"seq4 0.5348837 0.5121951 0.5135135 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))
def test_distance_d1_star2(self):
self.dist.set_disttype('d1_star2')
matrix = distmatrix.create(self.pep_records.id_list, self.dist)
exp = [
" 4",
"seq1 0.0000000 0.3404255 0.5436893 0.5609756",
"seq2 0.3404255 0.0000000 0.4130435 0.5384615",
"seq3 0.5436893 0.4130435 0.0000000 0.5205479",
"seq4 0.5609756 0.5384615 0.5205479 0.0000000"
]
self.assertEqual(matrix.format(), "\n".join(exp))