def test__calculate_composition(self):
d = os.path.dirname(os.path.abspath(__file__))
f = "{0}/test_data/composition_some_shortened.fa".format(d)
seqs = SeqIO.parse(f, "fasta")
feature_mapping, counter = generate_feature_mapping(4)
seq_strings = {}
for i, s in enumerate(seqs):
seq_strings[s.id] = str(s.seq).upper()
composition, contig_lengths = _calculate_composition(f, 0, 4)
# Make sure the count is correct for one specific kmer
kmer_s = ('A', 'C', 'G', 'T')
for seq_id, s in seq_strings.items():
c = count_substrings(s, "".join(kmer_s))
assert_equal(composition.loc[seq_id, feature_mapping[kmer_s]],
c + 1)
# Check that non palindromic kmers works as well:
kmer_s = ('A', 'G', 'G', 'G')
reverse_kmer_s = ('C', 'C', 'C', 'T')
for seq_id, s in seq_strings.items():
c_1 = count_substrings(s, "".join(kmer_s))
c_2 = count_substrings(s, "".join(reverse_kmer_s))
assert_equal(composition.loc[seq_id, feature_mapping[kmer_s]],
c_1 + c_2 + 1)
def test__calculate_composition(self):
d = os.path.dirname(os.path.abspath(__file__))
f = "{0}/test_data/composition_some_shortened.fa".format(d)
seqs = SeqIO.parse(f, "fasta")
feature_mapping, counter = generate_feature_mapping(4)
seq_strings = {}
for i, s in enumerate(seqs):
seq_strings[s.id] = str(s.seq).upper()
composition, contig_lengths = _calculate_composition(f, 0, 4)
# Make sure the count is correct for one specific kmer
kmer_s = ('A', 'C', 'G', 'T')
for seq_id, s in seq_strings.iteritems():
c = count_substrings(s, "".join(kmer_s))
assert_equal(composition.ix[seq_id, feature_mapping[kmer_s]], c+1)
# Check that non palindromic kmers works as well:
kmer_s = ('A', 'G', 'G', 'G')
reverse_kmer_s = ('C', 'C', 'C', 'T')
for seq_id, s in seq_strings.iteritems():
c_1 = count_substrings(s, "".join(kmer_s))
c_2 = count_substrings(s, "".join(reverse_kmer_s))
assert_equal(composition.ix[seq_id, feature_mapping[kmer_s]], c_1 + c_2 + 1)
def test_generate_feature_mapping(self):
feature_mapping, counter = generate_feature_mapping(2)
assert_equal(counter, 10)
assert_equal(len(list(feature_mapping.keys())), 16)
assert_true(('A', 'A') in feature_mapping)
def test_generate_feature_mapping(self):
feature_mapping, counter = generate_feature_mapping(2)
assert_equal(counter, 10)
assert_equal(len(feature_mapping.keys()), 16)
assert_true('AA' in feature_mapping)