def test_unequal_input(self):
sequences = [
"AATGA",
"AAAG",
"ACA",
]
output = {
0: {
'A': 3
},
1: {
'C': 1,
'A': 2
},
2: {
'T': 1,
'A': 2
},
3: {
'G': 2
},
4: {
'A': 1
},
}
assert FASTA_consensus.merge_FASTAs(sequences) == output
def test_with_headers(self):
sequences = [
">seq1",
"ACTG",
">seq2",
"AATG",
">seq3",
"ACAG",
]
output = {
0: {
'A': 3
},
1: {
'C': 2,
'A': 1
},
2: {
'T': 2,
'A': 1
},
3: {
'G': 3
},
}
assert FASTA_consensus.merge_FASTAs(sequences) == output
def test_gap_merge(self):
input_dict = {'A': 2, 'C': 3, 'G': 4, 'T': 5, '-': 6, 'N': 7}
output = frequency(Pos=1,
A=7.41,
C=11.11,
G=14.81,
T=18.52,
Gap=48.15,
Depth=27,
RefN='Gap')
assert FASTA_consensus.get_base_frequency(input_dict, 1) == output
def test_basic(self):
input_dict = {'C': 2, 'A': 1}
output = frequency(Pos=1,
A=33.33,
C=66.67,
G=0,
T=0,
Gap=0,
Depth=3,
RefN='C')
assert FASTA_consensus.get_base_frequency(input_dict, 1) == output
def test_simple_case(self):
input_dict = {
1: {
'A': 3
},
2: {
'C': 2,
'A': 1
},
3: {
'T': 2,
'A': 1
},
4: {
'G': 3
},
}
output = "ACTG"
assert FASTA_consensus.make_consensus(input_dict) == output
def test_again(self):
input_dict = {
1: {
'A': 3
},
2: {
'C': 1,
'A': 2
},
3: {
'T': 1,
'A': 2
},
4: {
'G': 3
},
}
output = "AAAG"
assert FASTA_consensus.make_consensus(input_dict) == output
def test_skip_gap(self):
input_dict = {
0: {
'C': 2,
'A': 1
},
1: {
'A': 2,
'C': 3,
'G': 4,
'T': 5,
'-': 6,
'N': 7
},
2: {
'C': 2,
'A': 1
},
}
freq1 = frequency(Pos=1,
A=33.33,
C=66.67,
G=0,
T=0,
Gap=0,
Depth=3,
RefN='C')
freq2 = frequency(Pos=2,
A=33.33,
C=66.67,
G=0,
T=0,
Gap=0,
Depth=3,
RefN='C')
output = [freq1, freq2]
assert FASTA_consensus.make_frequency_matrix(input_dict) == output
def test_complete_gap_not_returned(self):
input_dict = {
1: {
'A': 3
},
2: {
'-': 3
},
3: {
'T': 1,
'A': 2
},
4: {
'G': 2
},
5: {
'A': 1
},
}
output = "AAGA"
assert FASTA_consensus.make_consensus(input_dict) == output
def test_unequal_input(self):
input_dict = {
1: {
'A': 3
},
2: {
'C': 1,
'A': 2
},
3: {
'T': 1,
'A': 2
},
4: {
'G': 2
},
5: {
'A': 1
},
}
output = "AAAGA"
assert FASTA_consensus.make_consensus(input_dict) == output
def test_again(self):
sequences = [
"AATG",
"AAAG",
"ACAG",
]
output = {
0: {
'A': 3
},
1: {
'C': 1,
'A': 2
},
2: {
'T': 1,
'A': 2
},
3: {
'G': 3
},
}
assert FASTA_consensus.merge_FASTAs(sequences) == output