def create_seqstructs(cfo, numclusts):
seqstructs = []
# read in first cluster and struct
currclust = cfo.readline().strip(">").strip()
struct = cfo.readline().strip()
seqs = []
for header, seq in MinimalFastaParser(cfo):
if "cluster_" in header:
aln = LoadSeqs(data=seqs, moltype=RNA)
seqstructs.append(
SeqStructure(struct, ''.join(aln.majorityConsensus()),
currclust))
# move on to next structgroup
struct = seq
seqs = []
currclust = header
else:
seqs.append((header, seq))
aln = LoadSeqs(data=seqs, moltype=RNA)
seqstructs.append(
SeqStructure(struct, ''.join(aln.majorityConsensus()), currclust))
if len(seqstructs) != numclusts:
raise AssertionError("%i structures, %i clusters. Not all clusters "
"folded!" % (len(seqstructs), numclusts))
return seqstructs
def test_replaceSeqs(self):
"""synchronize gaps between protein seqs and codon seqs"""
pd = {
'FlyingFox': 'C-TNAH',
'DogFaced': 'CGTNT-',
'FreeTaile': '-GTDTH',
'LittleBro': 'C-TD-H',
'TombBat': 'C--STH'
}
pal = LoadSeqs(moltype=PROTEIN, data=pd)
cu = {
'TombBat': 'TGTAGTACTCAT',
'FreeTaile': 'GGCACAGATACTCAT',
'FlyingFox': 'TGTACAAATGCTCAT',
'LittleBro': 'TGTACAGATCAT',
'DogFaced': 'TGTGGCACAAATACT'
}
co = LoadSeqs(moltype=DNA, data=cu, aligned=False)
cal = pal.replaceSeqs(co)
result = cal.todict()
for taxon, expected_sequence in [('FlyingFox', 'TGT---ACAAATGCTCAT'),
('DogFaced', 'TGTGGCACAAATACT---'),
('FreeTaile', '---GGCACAGATACTCAT'),
('LittleBro', 'TGT---ACAGAT---CAT'),
('TombBat', 'TGT------AGTACTCAT')]:
self.assertEqual(result[taxon], expected_sequence)
def test_split_fasta_diff_num_seqs_per_file(self):
"""split_fasta funcs as expected when diff num seqs go to each file
"""
_, filename_prefix = mkstemp(dir=get_qiime_temp_dir(),
prefix='split_fasta_tests',
suffix='')
close(_)
infile = [
'>seq1', 'AACCTTAA', '>seq2', 'TTAACC', 'AATTAA', '>seq3',
'CCTT--AA'
]
actual = split_fasta(infile, 2, filename_prefix)
actual_seqs = []
for fp in actual:
actual_seqs += list(open(fp))
remove_files(actual)
expected = ['%s.%d.fasta' % (filename_prefix, i) for i in range(2)]
# list of file paths is as expected
self.assertEqual(actual, expected)
# building seq collections from infile and the split files result in
# equivalent seq collections
self.assertEqual(LoadSeqs(data=infile, aligned=False),
LoadSeqs(data=actual_seqs, aligned=False))
def test_alignadd(self):
"""testing adding one alignment to another."""
align1= LoadSeqs(data={'a': 'AAAA', 'b': 'TTTT', 'c': 'CCCC'})
align2 = LoadSeqs(data={'a': 'GGGG', 'b': '----', 'c': 'NNNN'})
align = align1 + align2
concatdict = align.todict()
self.assertEqual(concatdict, {'a': 'AAAAGGGG', 'b': 'TTTT----', 'c': 'CCCCNNNN'})
def test_reversecomplement(self):
"""test reverse complementing of Alignments and SequenceCollection."""
dna = {
'seq1': '--ACGT--GT---',
'seq2': 'TTACGTA-GT---',
'seq3': '--ACGTA-GCC--'
}
dna_rc = {
'seq1': '---AC--ACGT--',
'seq2': '---AC-TACGTAA',
'seq3': '--GGC-TACGT--'
}
# alignment with gaps
aln = LoadSeqs(data=dna, moltype=DNA)
aln_rc = aln.rc()
self.assertEqual(aln_rc.todict(), dna_rc)
# check collection, with gaps
coll = LoadSeqs(data=dna, moltype=DNA, aligned=False)
coll_rc = coll.rc()
self.assertEqual(coll_rc.todict(), dna_rc)
self.assertEqual(coll_rc.todict(), coll.reversecomplement().todict())
# collection with no gaps
dna = {'seq1': 'ACGTGT', 'seq2': 'TTACGTAGT', 'seq3': 'ACGTAGCC'}
dna_rc = {'seq1': 'ACACGT', 'seq2': 'ACTACGTAA', 'seq3': 'GGCTACGT'}
coll = LoadSeqs(data=dna, moltype=DNA, aligned=False)
coll_rc = coll.rc()
self.assertEqual(coll_rc.todict(), dna_rc)
def test_split_fasta_diff_num_seqs_per_file_alt(self):
"""split_fasta funcs always catches all seqs
"""
# start with 59 seqs (b/c it's prime, so should make more
# confusing splits)
in_seqs = LoadSeqs(data=[('seq%s' % k, 'AACCTTAA') for k in range(59)])
infile = in_seqs.toFasta().split('\n')
# test seqs_per_file from 1 to 1000
for i in range(1, 1000):
_, filename_prefix = mkstemp(dir=get_qiime_temp_dir(),
prefix='split_fasta_tests',
suffix='')
close(_)
actual = split_fasta(infile, i, filename_prefix)
actual_seqs = []
for fp in actual:
actual_seqs += list(open(fp))
# remove the files now, so if the test fails they still get
# cleaned up
remove_files(actual)
# building seq collections from infile and the split files result in
# equivalent seq collections
self.assertEqual(LoadSeqs(data=infile, aligned=False),
LoadSeqs(data=actual_seqs, aligned=False))
def setUp(self):
self.pynast_test1_input_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.fasta')
open(self.pynast_test1_input_fp, 'w').write(pynast_test1_input_fasta)
self.pynast_test1_template_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test1_template_fp, 'w').\
write(pynast_test1_template_fasta)
self.pynast_test_template_w_dots_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test_template_w_dots_fp, 'w').\
write(pynast_test1_template_fasta.replace('-', '.'))
self.pynast_test_template_w_u_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test_template_w_u_fp, 'w').\
write(pynast_test1_template_fasta.replace('T', 'U'))
self.pynast_test_template_w_lower_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test_template_w_lower_fp, 'w').\
write(pynast_test1_template_fasta.lower())
# create temp file names (and touch them so we can reliably
# clean them up)
self.result_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.fasta')
open(self.result_fp, 'w').close()
self.failure_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.fasta')
open(self.failure_fp, 'w').close()
self.log_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.log')
open(self.log_fp, 'w').close()
self._paths_to_clean_up = [
self.pynast_test1_input_fp,
self.result_fp,
self.failure_fp,
self.log_fp,
self.pynast_test1_template_fp,
self.pynast_test_template_w_dots_fp,
self.pynast_test_template_w_u_fp,
self.pynast_test_template_w_lower_fp
]
self.pynast_test1_aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len': 15,
})
self.pynast_test1_expected_aln = \
LoadSeqs(
data=pynast_test1_expected_alignment,
aligned=DenseAlignment)
self.pynast_test1_expected_fail = \
LoadSeqs(data=pynast_test1_expected_failure, aligned=False)
def test_withoutAnyGaps(self):
"""test removal of all gaps (any entries in alignment column are gaps)"""
alignment = LoadSeqs(data={'seq1': '--ACGT--GT---', 'seq2': '--ACGTA-GT---', 'seq3': '--ACGTA-GT---'})
align_dict = alignment.omitGapPositions(allowed_gap_frac=0).todict()
self.assertEqual(align_dict, {'seq1':'ACGTGT', 'seq2':'ACGTGT', 'seq3':'ACGTGT'})
alignment = LoadSeqs(data={'seq1': 'ACGT', 'seq2': '----', 'seq3': '----'})
align_dict = alignment.omitGapPositions(allowed_gap_frac=0).todict()
self.assertEqual(align_dict, {'seq1':'', 'seq2':'', 'seq3':''})
def setUp(self):
self.al = LoadSeqs(data = {'a':'GTACGTACGATC',
'b':'GTACGTACGTAC',
'c':'GTACGTACGTTC',
'e':'GTACGTACTGGT'})
self.collection = LoadSeqs(data = {'a':'GTACGTACGATC',
'b':'GTACGTACGTAC',
'c':'GTACGTACGTTC',
'e':'GTACGTACTGGT'}, aligned=False)
def __call__(self, seq_path, result_path=None, log_path=None,
failure_path=None):
# load candidate sequences
seq_file = open(seq_path, 'U')
candidate_sequences = parse_fasta(seq_file)
# load template sequences
template_alignment = []
template_alignment_fp = self.Params['template_filepath']
for seq_id, seq in parse_fasta(open(template_alignment_fp)):
# replace '.' characters with '-' characters
template_alignment.append((seq_id, seq.replace('.', '-').upper()))
try:
template_alignment = LoadSeqs(data=template_alignment, moltype=DNA,
aligned=DenseAlignment)
except KeyError as e:
raise KeyError('Only ACGT-. characters can be contained in template alignments.' +
' The offending character was: %s' % e)
# initialize_logger
logger = NastLogger(log_path)
# get function for pairwise alignment method
pairwise_alignment_f = pairwise_alignment_methods[
self.Params['pairwise_alignment_method']]
pynast_aligned, pynast_failed = pynast_seqs(
candidate_sequences,
template_alignment,
min_pct=self.Params['min_pct'],
min_len=self.Params['min_len'],
align_unaligned_seqs_f=pairwise_alignment_f,
logger=logger,
temp_dir=get_qiime_temp_dir())
logger.record(str(self))
if failure_path is not None:
fail_file = open(failure_path, 'w')
for seq in pynast_failed:
fail_file.write(seq.toFasta())
fail_file.write('\n')
fail_file.close()
if result_path is not None:
result_file = open(result_path, 'w')
for seq in pynast_aligned:
result_file.write(seq.toFasta())
result_file.write('\n')
result_file.close()
return None
else:
try:
return LoadSeqs(data=pynast_aligned, aligned=DenseAlignment)
except ValueError:
return {}
def setUp(self):
"""Sets up environment for tests
"""
self.random_seq = LoadSeqs(data=\
'>seq0\nACUGCGCGGAUCGAUCGAUCGAUCGAUGCAUUUUACGAUCGCCA\n', aligned=False)
self.rrna = LoadSeqs(data=RRNA, aligned=False)
self.rrna_aln = LoadSeqs(data=REF_ALN)
self.seq_db_path = os.path.join(ABSPATH, 'test_data',
'Rfam10_part.fasta')
def test_call_write_to_file(self):
"""ReferenceRepSetPicker.__call__ otu map correctly written to file"""
app = ReferenceRepSetPicker(params={'Algorithm':'first',
'ChoiceF':first_id})
app(self.tmp_seq_filepath,
self.tmp_otu_filepath,
self.ref_seq_filepath,
result_path=self.result_filepath)
exp = rep_seqs_reference_result_file_exp
self.assertEqual(LoadSeqs(self.result_filepath,aligned=False),
LoadSeqs(data=exp,aligned=False))
def test_translate(self):
for seqs in [
{'seq1': 'GATTTT', 'seq2': 'GATC??'},
{'seq1': 'GAT---', 'seq2': '?GATCT'}]:
alignment = LoadSeqs(data=seqs, moltype=DNA)
self.assertEqual(len(alignment.getTranslation()), 2)
# check for a failure when no moltype specified
alignment = LoadSeqs(data=seqs)
try:
peps = alignment.getTranslation()
except AttributeError:
pass
def optimization(result, aln, tree1, tree2):
# get the sites for each tree according to the assignments
aln1 = LoadSeqs(data=[('a', ''), ('c', ''), ('b', ''), ('d', '')],
moltype=DNA)
aln2 = LoadSeqs(data=[('a', ''), ('c', ''), ('b', ''), ('d', '')],
moltype=DNA)
for i in range(len(aln)):
if (result[i] == 1):
aln1 = aln1 + aln[i]
if (result[i] == 2):
aln2 = aln2 + aln[i]
if (result[i] == 0):
aln1 = aln1 + aln[i]
aln2 = aln2 + aln[i]
tree_parameter = [[], []]
modle = JC69()
# calculate the likelihood and do optimization. optimise will generates
# new tree parameters
lf1 = modle.makeLikelihoodFunction(tree1)
lf1.setAlignment(aln1)
lf1.optimise(local=True)
likelihood1 = lf1.getLogLikelihood()
# new tree parameters generates by optimise. As tree1/2 is symmetric, get
# p,q,r from 6 branch lengths
p1 = (lf1.getParamValue('length', 'a') +
lf1.getParamValue('length', 'c')) / 2.0
q1 = (lf1.getParamValue('length', 'b') +
lf1.getParamValue('length', 'd')) / 2.0
r1 = lf1.getParamValue('length', 'edge.1') + \
lf1.getParamValue('length', 'edge.0')
lf2 = modle.makeLikelihoodFunction(tree2)
lf2.setAlignment(aln2)
lf2.optimise(local=True)
likelihood2 = lf2.getLogLikelihood()
p2 = (lf2.getParamValue('length', 'a') +
lf2.getParamValue('length', 'c')) / 2.0
q2 = (lf2.getParamValue('length', 'b') +
lf2.getParamValue('length', 'd')) / 2.0
r2 = lf2.getParamValue('length', 'edge.1') + \
lf2.getParamValue('length', 'edge.0')
# return the new tree_parameter. As likelihood is in log, so plus together
# get the total likelihood for the whole sites
tree_parameter[0] = [p1, q1, r1]
tree_parameter[1] = [p2, q2, r2]
likelihood = likelihood1 + likelihood2
return tree_parameter, likelihood
def test_degap(self):
"""test stripping gaps from collections and alignments"""
aln = LoadSeqs(data={'seq1': '--ACGT--GT---', 'seq2': '--ACGTA-GT---',
'seq3': '--ACGTA-GT---'})
observed = aln.degap()
expect = {'seq1': 'ACGTGT', 'seq2': 'ACGTAGT', 'seq3': 'ACGTAGT'}
self.assertEqual(observed.todict(), expect)
collection = LoadSeqs(data={'seq1': '--ACGT--GT---',
'seq2': '--ACGTA-GT---', 'seq3': '--ACGTA-GT---'},
aligned=False, moltype=DNA)
observed = collection.degap()
self.assertEqual(observed.todict(), expect)
self.assertEqual(observed.MolType, DNA)
def test_withoutTerminalStopCodons(self):
"""test without terminal stop handling"""
seq_coll = LoadSeqs(data = {'seq1': 'ACGTAA', 'seq2': 'ACGACG',
'seq3': 'ACGCGT'}, moltype = DNA, aligned=False)
seq_coll = seq_coll.withoutTerminalStopCodons()
seqs = seq_coll.todict()
self.assertEqual(seqs['seq1'], 'ACG') # note: not 'acg---'
self.assertEqual(seqs['seq2'], 'ACGACG')
aln = LoadSeqs(data = {'seq1': 'ACGTAA', 'seq2': 'ACGTGA',
'seq3': 'ACGTAA'}, moltype = DNA)
aln = aln.withoutTerminalStopCodons()
seqs = aln.todict()
self.assertEqual(seqs['seq1'], 'ACG') # note: not 'acg---'
self.assertEqual(seqs['seq2'], 'ACG')
self.assertEqual(seqs['seq3'], 'ACG')
def filter_samples(prefs, data, dir_path='', filename=None):
"""processes the filtering of the otus file and representative seq set, then
writes filtered otus and filtered representative seq set files"""
aln = data['aln']
otus = data['otus']
# filter the otus file based on which samples to remove
new_otus_list = filter_otus(otus, prefs)
filtered_otus_output_filepath = '%s/%s_sfiltered_otus.txt' \
% (dir_path, filename)
filtered_otus_output_filepath = open(filtered_otus_output_filepath, 'w')
# Write out a new otus file
for key in (new_otus_list):
filtered_otus_output_filepath.write(key[0])
for j in key[1]:
filtered_otus_output_filepath.write('\t' + str(j))
filtered_otus_output_filepath.write('\n')
filtered_otus_output_filepath.close()
# filter seq set
filtered_seqs, removed_seqs = filter_aln_by_otus(aln, prefs)
# write a fasta containing list of sequences removed from
# representative set
try:
removed_seqs = LoadSeqs(data=removed_seqs, aligned=False)
except:
raise ValueError(
'No sequences were removed. Did you specify the correct Sample ID?')
output_filepath2 = '%s/%s_sremoved.fasta' % (dir_path, filename)
output_file2 = open(output_filepath2, 'w')
output_file2.write(removed_seqs.toFasta())
output_file2.close()
# write a fasta containing the filtered representative seqs
try:
filtered_seqs = LoadSeqs(data=filtered_seqs, aligned=False)
except:
raise ValueError(
'No sequences were remaining in the fasta file. Did you remove all Sample ID\'s?')
output_filepath = '%s/%s_sfiltered.fasta' % (dir_path, filename)
output_file = open(output_filepath, 'w')
output_file.write(filtered_seqs.toFasta())
output_file.close()
def pair_hmm_align_unaligned_seqs(seqs, moltype, params={}):
"""
This needs to be moved to cogent.align.align
"""
seqs = LoadSeqs(data=seqs, moltype=moltype, aligned=False)
try:
s1, s2 = seqs.values()
except ValueError:
raise ValueError,\
"Pairwise aligning of seqs requires exactly two seqs."
try:
gap_open = params['gap_open']
except KeyError:
gap_open = 5
try:
gap_extend = params['gap_extend']
except KeyError:
gap_extend = 2
try:
score_matrix = params['score_matrix']
except KeyError:
score_matrix = make_dna_scoring_dict(\
match=1,transition=-1,transversion=-1)
return global_pairwise(s1, s2, score_matrix, gap_open, gap_extend)
def test_logdet_variance(self):
"""calculate logdet variance consistent with hand calculation"""
data = [
('seq1',
"GGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT"
),
('seq2',
"TAAAAAAAAAAGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCC"
)
]
aln = LoadSeqs(data=data, moltype=DNA)
logdet_calc = LogDetPair(moltype=DNA, alignment=aln)
logdet_calc.run(use_tk_adjustment=True, show_progress=False)
self.assertEqual(logdet_calc.Variances[1, 1], None)
index = dict(zip('ACGT', range(4)))
J = numpy.zeros((4, 4))
for p in zip(data[0][1], data[1][1]):
J[index[p[0]], index[p[1]]] += 1
for i in range(4):
if J[i, i] == 0:
J[i, i] += 0.5
J /= J.sum()
M = numpy.linalg.inv(J)
var = 0.
for i in range(4):
for j in range(4):
var += M[j, i]**2 * J[i, j] - 1
var /= 16 * len(data[0][1])
logdet_calc.run(use_tk_adjustment=False, show_progress=False)
dists = logdet_calc.getPairwiseDistances()
self.assertFloatEqual(logdet_calc.Variances[1, 1], var, eps=1e-3)
def getResult(self, aln_path, *args, **kwargs):
"""Returns alignment from sequences.
Currently does not allow parameter tuning of program and uses
default parameters -- this is bad and should be fixed.
#TODO: allow command-line access to important aln params.
"""
module = self.Params['Module']
# standard qiime says we just consider the first word as the unique ID
# the rest of the defline of the fasta alignment often doesn't match
# the otu names in the otu table
seqs = LoadSeqs(aln_path,
Aligned=True,
label_to_name=lambda x: x.split()[0])
result = module.build_tree_from_alignment(seqs, moltype=DNA)
try:
root_method = kwargs['root_method']
if root_method == 'midpoint':
result = root_midpt(result)
elif root_method == 'tree_method_default':
pass
except KeyError:
pass
return result
def BestLogLikelihood(aln,
alphabet=None,
exclude_chars=None,
allowed_chars='ACGT',
motif_length=None,
return_length=False):
"""returns the best log-likelihood according to Goldman 1993.
Arguments:
- alphabet: a sequence alphabet object.
- motif_length: 1 for nucleotide, 2 for dinucleotide, etc ..
- exclude_chars: a series of characters used to exclude motifs
- allowed_chars: only motifs that contain a subset of these are
allowed
- return_length: whether to also return the number of alignment columns
"""
assert alphabet or motif_length, "Must provide either an alphabet or a"\
" motif_length"
# need to use the alphabet, so we can enforce character compliance
if alphabet:
kwargs = dict(moltype=alphabet.MolType)
motif_length = alphabet.getMotifLen()
else:
kwargs = {}
aln = LoadSeqs(data=aln.todict(), **kwargs)
columns = aligned_columns_to_rows(aln, motif_length, exclude_chars,
allowed_chars)
num_cols = len(columns)
log_likelihood = get_G93_lnL_from_array(columns)
if return_length:
return log_likelihood, num_cols
return log_likelihood
def test_getBySequenceAnnotation(self):
aln = LoadSeqs(data={'a': 'ATCGAAATCGAT', 'b': 'ATCGA--TCGAT'})
b = aln.getSeq('b')
b.addAnnotation(Feature, 'test_type', 'test_label', [(4, 6)])
answer = aln.getBySequenceAnnotation('b', 'test_type')[0].todict()
self.assertEqual(answer, {'b': 'A--T', 'a': 'AAAT'})
def test_paralinear_variance(self):
"""calculate paralinear variance consistent with hand calculation"""
data = [
('seq1',
"GGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT"
),
('seq2',
"TAAAAAAAAAAGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCC"
)
]
aln = LoadSeqs(data=data, moltype=DNA)
paralinear_calc = ParalinearPair(moltype=DNA, alignment=aln)
paralinear_calc.run(show_progress=False)
index = dict(zip('ACGT', range(4)))
J = numpy.zeros((4, 4))
for p in zip(data[0][1], data[1][1]):
J[index[p[0]], index[p[1]]] += 1
for i in range(4):
if J[i, i] == 0:
J[i, i] += 0.5
J /= J.sum()
M = numpy.linalg.inv(J)
f = J.sum(1), J.sum(0)
var = 0.
for i in range(4):
for j in range(4):
var += M[j, i]**2 * J[i, j]
var -= 1 / numpy.sqrt(f[0][i] * f[1][i])
var /= 16 * len(data[0][1])
self.assertFloatEqual(paralinear_calc.Variances[1, 1], var, eps=1e-3)
def test_setMotifProbs(self):
"""Mprobs supplied to the parameter controller"""
model = cogent.evolve.substitution_model.Nucleotide(model_gaps=True,
motif_probs=None)
lf = model.makeLikelihoodFunction(self.tree,
motif_probs_from_align=False)
mprobs = {'A': 0.1, 'C': 0.2, 'G': 0.2, 'T': 0.5, '-': 0.0}
lf.setMotifProbs(mprobs)
self.assertEqual(lf.getMotifProbs(), mprobs)
lf.setMotifProbsFromData(self.al[:1], is_const=True)
self.assertEqual(lf.getMotifProbs()['G'], 0.6)
lf.setMotifProbsFromData(self.al[:1], pseudocount=1)
self.assertNotEqual(lf.getMotifProbs()['G'], 0.6)
# test with consideration of ambiguous states
al = LoadSeqs(data={
'seq1': 'ACGTAAGNA',
'seq2': 'ACGTANGTC',
'seq3': 'ACGTACGTG'
})
lf.setMotifProbsFromData(al, include_ambiguity=True, is_const=True)
motif_probs = dict(lf.getMotifProbs())
correct_probs = {
'A': 8.5 / 27,
'C': 5.5 / 27,
'-': 0.0,
'T': 5.5 / 27,
'G': 7.5 / 27
}
self.assertEqual(motif_probs, correct_probs)
self.assertEqual(sum(motif_probs.values()), 1.0)
def test_logdet_pair_aa(self):
"""logdet shouldn't fail to produce distances for aa seqs"""
aln = LoadSeqs('data/brca1_5.paml', moltype=DNA)
aln = aln.getTranslation()
logdet_calc = LogDetPair(moltype=PROTEIN, alignment=aln)
logdet_calc.run(use_tk_adjustment=True, show_progress=False)
dists = logdet_calc.getPairwiseDistances()
def setUp(self):
self.infernal_test1_input_fp = get_tmp_filename(
prefix='InfernalAlignerTests_', suffix='.fasta')
open(self.infernal_test1_input_fp,
'w').write(infernal_test1_input_fasta)
self.infernal_test1_template_fp = get_tmp_filename(
prefix='InfernalAlignerTests_', suffix='template.sto')
open(self.infernal_test1_template_fp,'w').\
write(infernal_test1_template_stockholm)
# create temp file names (and touch them so we can reliably
# clean them up)
self.result_fp = get_tmp_filename(prefix='InfernalAlignerTests_',
suffix='.fasta')
open(self.result_fp, 'w').close()
self.log_fp = get_tmp_filename(prefix='InfernalAlignerTests_',
suffix='.log')
open(self.log_fp, 'w').close()
self._paths_to_clean_up = [
self.infernal_test1_input_fp,
self.result_fp,
self.log_fp,
self.infernal_test1_template_fp,
]
self.infernal_test1_aligner = InfernalAligner({
'template_filepath':
self.infernal_test1_template_fp,
})
self.infernal_test1_expected_aln = \
LoadSeqs(data=infernal_test1_expected_alignment,aligned=Alignment,\
moltype=DNA)
def test_paralinear_pair_aa(self):
"""paralinear shouldn't fail to produce distances for aa seqs"""
aln = LoadSeqs('data/brca1_5.paml', moltype=DNA)
aln = aln.getTranslation()
paralinear_calc = ParalinearPair(moltype=PROTEIN, alignment=aln)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.getPairwiseDistances()
def test_paralinear_distance(self):
"""calculate paralinear variance consistent with hand calculation"""
data = [
('seq1',
"GGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT"
),
('seq2',
"TAAAAAAAAAAGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCC"
)
]
aln = LoadSeqs(data=data, moltype=DNA)
paralinear_calc = ParalinearPair(moltype=DNA, alignment=aln)
paralinear_calc.run(show_progress=False)
index = dict(zip('ACGT', range(4)))
J = numpy.zeros((4, 4))
for p in zip(data[0][1], data[1][1]):
J[index[p[0]], index[p[1]]] += 1
for i in range(4):
if J[i, i] == 0:
J[i, i] += 0.5
J /= J.sum()
M = numpy.linalg.inv(J)
f = J.sum(1), J.sum(0)
dist = -0.25 * numpy.log( numpy.linalg.det(J) / \
numpy.sqrt(f[0].prod() * f[1].prod()) )
self.assertFloatEqual(paralinear_calc.Dists[1, 1], dist, eps=1e-3)
def test_logdet_pair_dna(self):
"""logdet should produce distances that match MEGA"""
aln = LoadSeqs('data/brca1_5.paml', moltype=DNA)
logdet_calc = LogDetPair(moltype=DNA, alignment=aln)
logdet_calc.run(use_tk_adjustment=True, show_progress=False)
dists = logdet_calc.getPairwiseDistances()
all_expected = {
('Human', 'NineBande'): 0.075336929999999996,
('NineBande', 'DogFaced'): 0.0898575452,
('DogFaced', 'Human'): 0.1061747919,
('HowlerMon', 'DogFaced'): 0.0934480008,
('Mouse', 'HowlerMon'): 0.26422862920000001,
('NineBande', 'Human'): 0.075336929999999996,
('HowlerMon', 'NineBande'): 0.062202897899999998,
('DogFaced', 'NineBande'): 0.0898575452,
('DogFaced', 'HowlerMon'): 0.0934480008,
('Human', 'DogFaced'): 0.1061747919,
('Mouse', 'Human'): 0.26539976700000001,
('NineBande', 'HowlerMon'): 0.062202897899999998,
('HowlerMon', 'Human'): 0.036571181899999999,
('DogFaced', 'Mouse'): 0.2652555144,
('HowlerMon', 'Mouse'): 0.26422862920000001,
('Mouse', 'DogFaced'): 0.2652555144,
('NineBande', 'Mouse'): 0.22754789210000001,
('Mouse', 'NineBande'): 0.22754789210000001,
('Human', 'Mouse'): 0.26539976700000001,
('Human', 'HowlerMon'): 0.036571181899999999
}
for pair in dists:
got = dists[pair]
expected = all_expected[pair]
self.assertFloatEqual(got, expected)
def setUp(self):
#length all edges 1 except c=2. b&d transitions all other transverions
self.al = LoadSeqs(
data={'a':'tata', 'b':'tgtc', 'c':'gcga', 'd':'gaac', 'e':'gagc',})
self.tree = LoadTree(treestring='((a,b),(c,d),e);')
self.model = cogent.evolve.substitution_model.Nucleotide(
do_scaling=True, equal_motif_probs=True, model_gaps=True)