def test_consensus_with_only_partials():
nuc_seq = '-GG' # -> ?
expected_consensus = '?' # No complete reads, only partials.
amino = SeedAmino(None)
amino.count_aminos(nuc_seq, 4)
consensus = amino.get_consensus()
assert consensus == expected_consensus
def test_consensus():
nuc_seq1 = 'AAA' # -> K
nuc_seq2 = 'GGG' # -> G
expected_consensus = 'G'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 4)
amino.count_aminos(nuc_seq2, 5)
consensus = amino.get_consensus()
assert expected_consensus == consensus
def test_nucleotides():
nuc_seq1 = 'AAA' # -> K
nuc_seq2 = 'AAG' # -> K
expected_nuc_counts = '4,0,5,0'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 4)
amino.count_aminos(nuc_seq2, 5)
counts = amino.nucleotides[2].get_report()
assert expected_nuc_counts == counts
def test_missing_data():
""" Lower-case n represents a gap between the forward and reverse reads. """
nuc_seq = 'CTn'
expected_consensus = '?'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq, 1)
consensus = amino.get_consensus()
assert expected_consensus == consensus
def test_single_read():
""" Read a single codon, and report on counts.
Columns are: A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*
"""
nuc_seq = 'AAA' # -> K
expected_counts = '0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq, 8)
counts = amino.get_report()
assert expected_counts == counts
def test_add():
amino = SeedAmino(None)
amino.count_aminos('GGG', 4) # => G
other = SeedAmino(consensus_nuc_index=7)
other.count_aminos('AAA', 5) # => K
expected_counts = {'G': 4, 'K': 5}
expected_nucleotide_counts = {'G': 4, 'A': 5}
amino.add(other)
assert expected_counts == amino.counts
assert expected_nucleotide_counts == amino.nucleotides[0].counts
def test_overlap_partial_codon():
amino = SeedAmino(None)
amino.count_aminos('GGG', 4)
other = SeedAmino(consensus_nuc_index=7)
other.count_aminos('TA', 5)
expected_counts = {'G': 4}
expected_v3_overlap = 5
amino.count_overlap(other)
assert expected_counts == amino.counts
assert expected_v3_overlap == amino.v3_overlap
assert expected_v3_overlap == amino.nucleotides[0].v3_overlap
def test_ambiguous_data():
"""If a read is ambiguous, don't count it toward consensus."""
nuc_seq1 = 'Cnn' # -> ?
nuc_seq2 = 'AAA' # -> K
expected_consensus = 'K'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 9)
amino.count_aminos(nuc_seq2, 1)
consensus = amino.get_consensus()
assert expected_consensus == consensus
def test_same_amino_acid():
""" Read same codon twice, and report on counts.
Columns are: A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*
"""
nuc_seq1 = 'AAA' # -> K
nuc_seq2 = 'AAG' # -> K
expected_counts = '0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 4)
amino.count_aminos(nuc_seq2, 5)
counts = amino.get_report()
assert expected_counts == counts
def test_amino_repeat_nuc2():
""" Repeat last nucleotide in the codon.
Columns are: A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*
"""
nuc_seq1 = 'GAG' # -> E
nuc_seq2 = 'GAC' # -> D
expected_counts = '0,0,5,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 4)
amino.count_aminos(nuc_seq2, 5)
counts = amino.apply_repeat(2).get_report()
assert counts == expected_counts
def test_different_codon():
""" Read two different codons, and report on counts.
Columns are: A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*
"""
nuc_seq1 = 'AAA' # -> K
nuc_seq2 = 'GGG' # -> G
expected_counts = '0,0,0,0,0,5,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0'
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 8)
amino.count_aminos(nuc_seq2, 5)
counts = amino.get_report()
assert expected_counts == counts
def test_consensus_partial():
nuc_seq1 = 'AAA' # -> K
nuc_seq2 = '-GG' # -> ?
expected_consensus = 'K' # Complete reads always override partials.
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 4)
amino.count_aminos(nuc_seq2, 10)
consensus = amino.get_consensus()
assert consensus == expected_consensus
def test_consensus_mixture():
nuc_seq1 = 'AAA' # -> K
nuc_seq2 = 'GGG' # -> G
nuc_seq3 = 'TTT' # -> F
allowed_consensus_values = ('G', 'K')
amino = SeedAmino(None)
amino.count_aminos(nuc_seq1, 4)
amino.count_aminos(nuc_seq2, 4)
amino.count_aminos(nuc_seq3, 3)
consensus = amino.get_consensus()
assert consensus in allowed_consensus_values
def test_consensus_with_no_reads():
amino = SeedAmino(None)
consensus = amino.get_consensus()
assert consensus == '-'