def test_alignment_std_local(err):
A = Alphabet('ACGT')
M = MutationProcess(A, subst_probs=err, go_prob=err, ge_prob=err)
subst_scores, (go_score, ge_score) = M.log_odds_scores()
S = rand_seq(A, 100)
T, tx = M.mutate(S)
T = A.parse('A' * 100) + T + A.parse('G' * 100)
mutation_aln = Alignment(S, T, tx)
mutation_score = mutation_aln.calculate_score(subst_scores, go_score,
ge_score)
aligner = Aligner(S, T, subst_scores=subst_scores, go_score=go_score,
ge_score=ge_score, alnmode=STD_MODE, alntype=LOCAL)
with aligner:
reported_score = aligner.solve()
assert round(reported_score, 3) >= round(mutation_score, 3), \
'optimal alignment scores better than the known transcript'
alignment = aligner.traceback()
aln_score = alignment.calculate_score(subst_scores, go_score, ge_score)
assert round(aln_score, 3) == round(reported_score, 3), \
'The alignment score should be calculated correctly'
ori_len = Alignment.projected_len(alignment.transcript, on='origin')
mut_len = Alignment.projected_len(alignment.transcript, on='mutant')
assert ori_len <= len(S) and mut_len < len(T), \
'Local alignments do not cover the entirety of both sequences'
def test_pw_render_width():
A = Alphabet('ACGT')
N = 100
S = A.parse('A' * (2 * N))
tx, term_width = 'M' * N, N/2
aln = Alignment(S, S, tx, origin_start=N)
render = aln.render_term(margin=2*N, colored=False, term_width=term_width)
line_lens = [len(l) for l in render.rstrip().split('\n')]
assert all(length <= term_width for length in line_lens), \
'terminal width should be adjustable'
assert any(length == term_width for length in line_lens), \
'terminal width should be fully used'
assert len(set(line_lens)) <= 2, \
'alignments longer than terminal width should work'
def test_projected_aln_len():
assert Alignment.projected_len('MMM', on='origin') == 3
assert Alignment.projected_len('MMM', on='mutant') == 3
assert Alignment.projected_len('SMS', on='origin') == 3
assert Alignment.projected_len('SMS', on='mutant') == 3
assert Alignment.projected_len('DMS', on='origin') == 3
assert Alignment.projected_len('DMS', on='mutant') == 2
assert Alignment.projected_len('IMS', on='origin') == 2
assert Alignment.projected_len('IMS', on='mutant') == 3
def test_pw_render_longlet():
A = Alphabet(['00', '11'])
aln = Alignment(A.parse('0011'), A.parse('11'), 'DM')
assert '--11' in aln.render_term(colored=False), \
'alphabets with > 1 long letters should be rendered properly'
def test_pw_render_basic():
A = Alphabet('ACGT')
S = A.parse('AACT')
aln = Alignment(S, S, 'M' * len(S))
assert aln.render_term(colored=False).count('\033') == 0, \
'colored output should allow being turned off'
assert aln.render_term(colored=True).count('\033') > 0, \
'colored output should allow being turned on'
# validate input
with pytest.raises(AssertionError):
aln.render_term(margin=-1)
with pytest.raises(AssertionError):
aln.render_term(term_width=5)
aln = Alignment(S + S, S + S, 'M' * len(S), origin_start=len(S))
no_margin = aln.render_term(margin=0, colored=False)
assert '[%d]' % len(S) in no_margin, 'margin should allow being turned off'
with_margin = aln.render_term(margin=1, colored=False)
assert '[%d]' % (len(S) - 1) in with_margin, \
'margin should allow being turned on'
# shouldn't choke on too large margins
full_margin = aln.render_term(margin=30, colored=False)
assert str(S) + '.' * len(S) in full_margin, 'overhanging margins work'
assert len(set(len(l) for l in full_margin.rstrip().split('\n'))) == 1, \
'both lines of the output should have the same length'
# deletion:
# AACT
# AG-T
aln = Alignment(S + S, A.parse('AGT'), 'MSDM', origin_start=len(S))
with_del = aln.render_term(colored=False)
assert 'AG-T' in with_del, 'deletions are represented by - in mutant'
lines = with_del.rstrip().split('\n')
assert lines[0].index('C') == lines[1].index('-'), \
'deleted content and - should be aligned'
# shouldn't crash when printing deletions with color
aln.render_term(colored=True)
# insertion:
# AAC-T
# AACGT
aln = Alignment(S + S, A.parse('AACGT'), 'MMMIM', origin_start=len(S))
with_ins = aln.render_term(colored=False)
assert 'AAC-T' in with_ins, 'insertions are represented by - in origin'
lines = with_ins.rstrip().split('\n')
assert lines[0].index('-') == lines[1].index('G'), \
'inserted content and - should be aligned'
# shouldn't crash when printing with color
with_ins = aln.render_term(colored=True)