def test_paralinear_for_determinant_lte_zero(self):
"""returns distance of None if the determinant is <= 0"""
data = dict(seq1="AGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT",
seq2="TAAAAAAAAAAGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCC")
aln = LoadSeqs(data=data, moltype=DNA)
paralinear_calc = ParalinearPair(moltype=DNA, alignment=aln)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.getPairwiseDistances()
self.assertTrue(dists.values()[0] is None)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.getPairwiseDistances()
self.assertTrue(dists.values()[0] is None)
def test_paralinear_for_determinant_lte_zero(self):
"""returns distance of None if the determinant is <= 0"""
data = dict(
seq1=
"AGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT",
seq2=
"TAAAAAAAAAAGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCC")
aln = LoadSeqs(data=data, moltype=DNA)
paralinear_calc = ParalinearPair(moltype=DNA, alignment=aln)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.getPairwiseDistances()
self.assertTrue(dists.values()[0] is None)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.getPairwiseDistances()
self.assertTrue(dists.values()[0] is None)
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_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 get_paralinear_distances(gene, data_directory=None, third_position=False, **kw):
filenames = glob.glob(os.path.join(data_directory, gene+'.fasta*'))
assert len(filenames) == 1, 'Wrong number of alignment files for ' + gene
filename = filenames[0]
if filename.endswith('.fasta'):
with open(filename) as fastafile:
fastadata = fastafile.read()
elif filename.endswith('.fasta.gz'):
with GzipFile(filename) as fastafile:
fastadata = fastafile.read()
else:
raise RuntimeError(gene + ' file could not be read')
sequences = LoadSeqs(data=fastadata)
if third_position:
indices = [(i, i+1) for i in range(len(sequences))[2::3]]
pos3 = sequences.addFeature('pos3', 'pos3', indices)
sequences = pos3.getSlice()
sequences = sequences.filtered(lambda x: set(''.join(x)) <= set(DNA))
paralinear_calc = ParalinearPair(moltype=DNA, alignment=sequences)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.getPairwiseDistances()
return {frozenset(k):v for k, v in dists.items()}
