def test(self):
'''Test allele counts from read with indels
A A - - - - - G G T T T C C C
0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6
\___/ \___/ \___/ \___/ \___/ \__
0 1 2 3 4 5
--- GTT TCC
'''
counts = np.zeros((len(alphaal), (len(self.read.seq) // 3) + 3), int)
# Expected result
from Bio.Data.CodonTable import standard_dna_table
t = standard_dna_table.forward_table
counts_check = counts.copy()
codons = [(1, '---'), (3, 'GTT'), (4, 'TCC')]
for posc, codon in codons:
if codon == '---':
aa = alphaal.index('-')
else:
aa = alphaal.index(t[codon])
counts_check[aa, posc] += 1
# Call the function
get_allele_counts_aa_read(self.read, 0, 90, counts)
# Equality test (they are ints)
np.testing.assert_array_equal(counts, counts_check)
def test2(self):
'''Test allele counts from read with an out-of-frame insertion
In addition, the protein starts out-of-frame with the read.
A A A G T T T C C C
0 1 2 3 4 5 6 7 8 9 0
\___/ \___/ \___/ \__
0 1 2 3
TTC
'''
counts = np.zeros((len(alphaal), (len(self.read.seq) // 3) + 3), int)
# Expected result
from Bio.Data.CodonTable import standard_dna_table
t = standard_dna_table.forward_table
counts_check = counts.copy()
codons = [(2, 'TTC')]
for posc, codon in codons:
aa = alphaal.index(t[codon])
counts_check[aa, posc] += 1
# Call the function
get_allele_counts_aa_read(self.read, 0, 90, counts)
# Equality test (they are ints)
np.testing.assert_array_equal(counts, counts_check)
def test(self):
'''Test allele counts from match only'''
counts = np.zeros((len(alphaal), (len(self.read.seq) // 3) + 3), int)
# Expected result
from Bio.Data.CodonTable import standard_dna_table
t = standard_dna_table.forward_table
counts_check = counts.copy()
for pos in xrange(len(self.read.seq) // 3):
aa = alphaal.index(t[self.read.seq[3 * pos: 3 * (pos + 1)]])
counts_check[aa, pos] += 1
# Call the function
get_allele_counts_aa_read(self.read, 1, 90, counts)
# Equality test (they are ints)
np.testing.assert_array_equal(counts, counts_check)
def test1(self):
'''Test allele counts from read with an out-of-frame insertion'''
counts = np.zeros((len(alphaal), (len(self.read.seq) // 3) + 3), int)
# Expected result
from Bio.Data.CodonTable import standard_dna_table
t = standard_dna_table.forward_table
counts_check = counts.copy()
codons = ['AAA', 'GTT', 'TCC']
for posc, codon in enumerate(codons):
aa = alphaal.index(t[codon])
counts_check[aa, posc] += 1
# Call the function
get_allele_counts_aa_read(self.read, 1, 90, counts)
# Equality test (they are ints)
np.testing.assert_array_equal(counts, counts_check)
def test(self):
'''Test allele counts from read with an in-frame insertion'''
counts = np.zeros((len(alphaal), (len(self.read.seq) // 3) + 3), int)
# Expected result
from Bio.Data.CodonTable import standard_dna_table
t = standard_dna_table.forward_table
counts_check = counts.copy()
for pos in xrange(len(self.read.seq) // 3):
if 1 <= pos < 2:
continue
elif pos >= 2:
posc = pos - 1
else:
posc = pos
aa = alphaal.index(t[self.read.seq[3 * pos: 3 * (pos + 1)]])
counts_check[aa, posc] += 1
# Call the function
get_allele_counts_aa_read(self.read, 1, 90, counts)
# Equality test (they are ints)
np.testing.assert_array_equal(counts, counts_check)
