def test_init_one_parameter(self):
"""PairFrequency should interpret single parameter as pair probs"""
obs = PairFrequency('UCCC')
exp = Freqs({('U','U'):0.0625, ('U','C'):0.1875,
('C','U'):0.1875, ('C','C'):0.5625})
for k, v in exp.items():
self.assertEqual(v, obs[k])
for k, v in obs.items():
if k not in exp:
self.assertEqual(v, 0)
self.assertEqual(PairFrequency('UCCC', [('U','U'),('C','C')]), \
Freqs({('U','U'):0.1, ('C','C'):0.9}))
#check that the alphabets are right: should not raise error on
#incrementing characters already there, but should raise KeyError
#on anything that's missing.
p = PairFrequency('UCCC')
p[('U','U')] += 1
try:
p[('X','U')] += 1
except KeyError:
pass
else:
raise AssertionError, "Expected KeyError."
p = PairFrequency('UCCC', (('C','C'),))
p[('C','C')] += 1
try:
p[('U','U')] += 1
except KeyError:
pass
else:
raise AssertionError, "Expected KeyError."
def MagePointFromBaseFreqs(freqs, get_label=None, get_color=None, \
get_radius=None):
"""Returns a MagePoint from an object with counts for the bases.
get_label should be a function that calculates a label from the freqs.
If get_label is not supplied, checks freqs.Label, freqs.Species, freqs.Id,
freqs.Accession, and freqs.Name in that order. If get_label fails or none
of the attributes is found, no label is written.
get_color should be a function that calculates a color from the freqs.
Default is no color (i.e. the point has the color for the series), which
will also happen if get_color fails.
get_radius is similar to get_color.
"""
label = None
if get_label:
try:
label = get_label(freqs)
except:
pass #label will be assigned None below
else:
for attr in ['Label', 'Species', 'Id', 'Accession', 'Name']:
if hasattr(freqs, attr):
label = getattr(freqs, attr)
#keep going if the label is empty
if label is not None and label != '':
break
if not label and label != 0:
label = None
if get_color:
try:
color = get_color(freqs)
except:
color=None
else:
if hasattr(freqs, 'Color'):
color = freqs.Color
else:
color = None
if get_radius:
try:
radius = get_radius(freqs)
except:
radius=None
else:
if hasattr(freqs, 'Radius'):
try:
radius = float(freqs.Radius)
except:
radius = None
else:
radius = None
relevant = Freqs({'A':freqs.get('A',0), 'C':freqs.get('C',0),
'G':freqs.get('G',0), 'U':freqs.get('U',0) or freqs.get('T',0)})
relevant.normalize()
return MagePoint((relevant['A'],relevant['C'],relevant['G']), Label=label,\
Color=color, Radius=radius)
def test_known_vals(self):
"""Composition should return precalculated elements for known cases"""
self.assertEqual(len(Composition(5,1,"ACGU")), 969)
self.assertEqual(len(Composition(5,0,"ACGU")), 1771)
as_list = list(Composition(5,1,"ACGU"))
self.assertEqual(as_list[0], Freqs('A'*17+'CGU'))
self.assertEqual(as_list[-1], Freqs('U'*17+'ACG'))
def MagePointFromBaseFreqs(freqs, get_label=None, get_color=None, \
get_radius=None):
"""Returns a MagePoint from an object with counts for the bases.
get_label should be a function that calculates a label from the freqs.
If get_label is not supplied, checks freqs.Label, freqs.Species, freqs.Id,
freqs.Accession, and freqs.Name in that order. If get_label fails or none
of the attributes is found, no label is written.
get_color should be a function that calculates a color from the freqs.
Default is no color (i.e. the point has the color for the series), which
will also happen if get_color fails.
get_radius is similar to get_color.
"""
label = None
if get_label:
try:
label = get_label(freqs)
except:
pass #label will be assigned None below
else:
for attr in ['Label', 'Species', 'Id', 'Accession', 'Name']:
if hasattr(freqs, attr):
label = getattr(freqs, attr)
#keep going if the label is empty
if label is not None and label != '':
break
if not label and label != 0:
label = None
if get_color:
try:
color = get_color(freqs)
except:
color=None
else:
if hasattr(freqs, 'Color'):
color = freqs.Color
else:
color = None
if get_radius:
try:
radius = get_radius(freqs)
except:
radius=None
else:
if hasattr(freqs, 'Radius'):
try:
radius = float(freqs.Radius)
except:
radius = None
else:
radius = None
relevant = Freqs({'A':freqs.get('A',0), 'C':freqs.get('C',0),
'G':freqs.get('G',0), 'U':freqs.get('U',0) or freqs.get('T',0)})
relevant.normalize()
return MagePoint((relevant['A'],relevant['C'],relevant['G']), Label=label,\
Color=color, Radius=radius)
def kendalls_tau(x, y, return_p=True):
"""returns kendall's tau
Arguments:
- return_p: returns the probability from the normal approximation when
True, otherwise just returns tau"""
ranked = as_paired_ranks(x, y)
n = len(ranked)
denom = n * (n - 1) / 2
con = 0
discor = 0
x_tied = 0
y_tied = 0
for i in range(n - 1):
x_1 = ranked[i][0]
y_1 = ranked[i][1]
for j in range(i + 1, n):
x_2 = ranked[j][0]
y_2 = ranked[j][1]
x_diff = x_1 - x_2
y_diff = y_1 - y_2
if x_diff * y_diff > 0:
con += 1
elif x_diff and y_diff:
discor += 1
else:
if x_diff:
y_tied += 1
if y_diff:
x_tied += 1
diff = con - discor
total = con + discor
denom = ((total + y_tied) * (total + x_tied))**0.5
variance = (4 * n + 10) / (9 * n * (n - 1))
tau = diff / denom
stat = tau
if x_tied or y_tied:
x_tied = array([v for v in Freqs(x).itervalues() if v > 1])
y_tied = array([v for v in Freqs(y).itervalues() if v > 1])
t0 = n * (n - 1) / 2
t1 = sum(x_tied * (x_tied - 1)) / 2
t2 = sum(y_tied * (y_tied - 1)) / 2
stat = tau * sqrt((t0 - t1) * (t0 - t2))
v0 = n * (n - 1) * (2 * n + 5)
vt = sum(x_tied * (x_tied - 1) * (2 * x_tied + 5))
vu = sum(y_tied * (y_tied - 1) * (2 * y_tied + 5))
v1 = sum(x_tied * (x_tied - 1)) * sum(y_tied * (y_tied - 1))
v2 = sum(x_tied * (x_tied - 1) * (x_tied - 2)) * \
sum(y_tied * (y_tied - 1) * (y_tied - 2))
variance = (v0 - vt - vu) / 18 + v1 / (2 * n * (n - 1)) + v2 / (9 * n * \
(n - 1) * (n - 2))
if return_p:
return tau, zprob(stat / variance**0.5)
else:
return tau
def __init__(self, data=None, Info=None, **kwargs):
"""Intializes BaseUsage with data, either sequence or dict of freqs.
Ignores additional kwargs (e.g. to support copy).
Makes the _handler for delegator accessible with the name Info.
"""
if Info is None:
if hasattr(data, 'Info'):
Info = data.Info
else:
Info = InfoClass()
Delegator.__init__(self, Info)
Freqs.__init__(self, data or [], **kwargs)
def __init__(self, data=None, Info=None, **kwargs):
"""Intializes BaseUsage with data, either sequence or dict of freqs.
Ignores additional kwargs (e.g. to support copy).
Makes the _handler for delegator accessible with the name Info.
"""
if Info is None:
if hasattr(data, 'Info'):
Info = data.Info
else:
Info = InfoClass()
Delegator.__init__(self, Info)
Freqs.__init__(self, data or [], **kwargs)
def random_source(a, k, random_f=random):
"""Makes a random Markov source on alphabet a with memory k.
Specifically, for all words k, pr(i|k) = rand().
"""
result = dict.fromkeys(list(map(''.join, cartesian_product([a]*k))))
for k in result:
result[k] = Freqs(dict(list(zip(a, random_f(len(a))))))
return result
def toFreqs(self):
"""Returns a Freqs object based on the histogram.
Labels of Freqs will be _bins converted into strings
Values of Freqs will be the number of objects in a Bin
"""
result = Freqs()
for bin, values in self:
result[str(bin)] = len(values)
return result
def codons(self, genetic_code=SGC, codon_usage=_equal_codons):
"""Predicts most likely set of codon frequencies.
Optionally uses genetic_code (to figure out which codons belong
with each amino acid), and codon_usage (to get most likely codons for
each amino acid). Defaults are the standard genetic code and unbiased
codon frequencies.
"""
result = {}
normalized = Freqs(self)
normalized.normalize()
for aa, aa_freq in list(normalized.items()):
curr_codons = [c.upper().replace('T','U') for c in genetic_code[aa]]
if not curr_codons:
continue #code might be missing some amino acids?
curr_codon_freqs = Numbers([codon_usage[c] for c in curr_codons])
curr_codon_freqs.normalize()
for codon, c_freq in zip(curr_codons, curr_codon_freqs):
result[codon] = c_freq * aa_freq
return CodonUsage(result, self.info, genetic_code)
def codons(self, genetic_code=SGC, codon_usage=_equal_codons):
"""Predicts most likely set of codon frequencies.
Optionally uses genetic_code (to figure out which codons belong
with each amino acid), and codon_usage (to get most likely codons for
each amino acid). Defaults are the standard genetic code and unbiased
codon frequencies.
"""
result = {}
normalized = Freqs(self)
normalized.normalize()
for aa, aa_freq in normalized.items():
curr_codons = [c.upper().replace('T','U') for c in genetic_code[aa]]
if not curr_codons:
continue #code might be missing some amino acids?
curr_codon_freqs = Numbers([codon_usage[c] for c in curr_codons])
curr_codon_freqs.normalize()
for codon, c_freq in zip(curr_codons, curr_codon_freqs):
result[codon] = c_freq * aa_freq
return CodonUsage(result, self.info, genetic_code)
def apply_to(s):
if s and not case_sens:
used_s = [str(item).lower() for item in s]
else:
used_s = s
fd = Freqs(used_s)
value_list = [fd[i] for i in fd if i not in used_items]
if value_list:
count = reduce(add, value_list)
return count > x
else:
return False
def test_init(self):
"""Unpaired region should generate right freqs, even after change"""
freqs = Freqs({"C": 10, "U": 1, "A": 0})
r = UnpairedRegion("NN", freqs)
seq = r.Current
assert seq[0] in "CU"
assert seq[1] in "CU"
self.assertEqual(len(seq), 2)
fd = []
for i in range(1000):
r.refresh()
fd.append(str(seq))
fd = Freqs("".join(fd))
observed = [fd["C"], fd["U"]]
expected = [1800, 200]
self.assertSimilarFreqs(observed, expected)
self.assertEqual(fd["U"] + fd["C"], 2000)
freqs2 = Freqs({"A": 5, "U": 5})
r.Composition = freqs2
r.Template = "NNN" # note that changing the Template changes seq ref
seq = r.Current
self.assertEqual(len(seq), 3)
assert seq[0] in "AU"
assert seq[1] in "AU"
assert seq[2] in "AU"
fd = []
for i in range(1000):
r.refresh()
fd.append(str(seq))
fd = Freqs("".join(fd))
observed = [fd["A"], fd["U"]]
expected = [1500, 1500]
self.assertSimilarFreqs(observed, expected)
self.assertEqual(fd["A"] + fd["U"], 3000)
def calcFrequencies(self, delete_bad_suffixes=True):
"""For order k, gets the (k-1)-word frequencies plus what follows."""
#reset text if possible -- but it might just be a string, so don't
#complain if the reset fails.
overlapping=self.Overlapping
try:
self.Text.reset()
except AttributeError:
try:
self.Text.seek(0)
except AttributeError:
pass
k = self.Order
if k < 1: #must be 0 or '-1': just need to count single bases
self._first_order_frequency_calculation()
else: #need to figure out what comes after the first k bases
all_freqs = {}
for line in self.Text:
if not self.Linebreaks:
line = line.strip()
#skip the line if it's blank
if (not line):
continue
#otherwise, make a frequency distribution of symbols
end = len(line) - k
if overlapping:
rang=range(end)
else:
rang=range(0,end,(k+1))
for i in rang:
word, next = line[i:i+k], line[i+k]
curr = all_freqs.get(word, None)
if curr is None:
curr = Freqs({next:1})
all_freqs[word] = curr
else:
curr += next
if self._calc_entropy:
self.Entropy = self._entropy(all_freqs)
self.Frequencies = all_freqs
if delete_bad_suffixes:
self.deleteBadSuffixes()
self.RawCounts=deepcopy(all_freqs)
#preserve non-normalized freqs
for dist in list(self.Frequencies.values()):
dist.normalize()
def test_init(self):
"""Unpaired region should generate right freqs, even after change"""
freqs = Freqs({'C':10,'U':1, 'A':0})
r = UnpairedRegion('NN', freqs)
seq = r.Current
assert seq[0] in 'CU'
assert seq[1] in 'CU'
self.assertEqual(len(seq), 2)
fd = []
for i in range(1000):
r.refresh()
fd.append(str(seq))
fd = Freqs(''.join(fd))
observed = [fd['C'], fd['U']]
expected = [1800, 200]
self.assertSimilarFreqs(observed, expected)
self.assertEqual(fd['U'] + fd['C'], 2000)
freqs2 = Freqs({'A':5, 'U':5})
r.Composition = freqs2
r.Template = 'NNN' #note that changing the Template changes seq ref
seq = r.Current
self.assertEqual(len(seq), 3)
assert seq[0] in 'AU'
assert seq[1] in 'AU'
assert seq[2] in 'AU'
fd = []
for i in range(1000):
r.refresh()
fd.append(str(seq))
fd = Freqs(''.join(fd))
observed = [fd['A'], fd['U']]
expected = [1500, 1500]
self.assertSimilarFreqs(observed, expected)
self.assertEqual(fd['A'] + fd['U'], 3000)
def _first_order_frequency_calculation(self):
"""Handles single-character calculations, which are independent.
Specifically, don't need to take into account any other characters, and
can just feed the whole thing into a single Freqs.
"""
freqs = Freqs('')
for line in self.Text:
freqs += line
#get rid of line breaks if necessary
if not self.Linebreaks:
for badkey in ['\r', '\n']:
try:
del freqs[badkey]
except KeyError:
pass #don't care if there weren't any
#if order is negative, equalize the frequencies
if self.Order < 0:
for key in freqs:
freqs[key] = 1
self.RawCounts= {'':deepcopy(freqs)}
freqs.normalize()
self.Frequencies = {'':freqs}
def test_init(self):
"""ConstantRegion should always return current template."""
#test blank region model
r = ConstantRegion()
self.assertEqual(str(r.Current), '')
self.assertEqual(len(r), 0)
#now assign it to a template
r.Template = ('ACGUUCGA')
self.assertEqual(str(r.Current), 'ACGUUCGA')
self.assertEqual(len(r), len('ACGUUCGA'))
#check that refresh doesn't break anything
r.refresh()
self.assertEqual(str(r.Current), 'ACGUUCGA')
self.assertEqual(len(r), len('ACGUUCGA'))
#check composition
self.assertEqual(r.Composition, None)
d = {'A':3, 'U':10}
r.Composition = Freqs(d)
self.assertEqual(r.Composition, d)
#check that composition doesn't break the update
r.refresh()
self.assertEqual(str(r.Current), 'ACGUUCGA')
self.assertEqual(len(r), len('ACGUUCGA'))
def MagePointFromBaseFreqs(freqs, get_label=None, get_color=None, get_radius=None):
"""Returns a MagePoint from an object with counts for the bases.
get_label should be a function that calculates a label from the freqs.
If get_label is not supplied, checks freqs.Label, freqs.Species, freqs.Id,
freqs.Accession, and freqs.Name in that order. If get_label fails or none
of the attributes is found, no label is written.
get_color should be a function that calculates a color from the freqs.
Default is no color (i.e. the point has the color for the series), which
will also happen if get_color fails.
get_radius is similar to get_color.
"""
label = None
if get_label:
try:
label = get_label(freqs)
except:
pass # label will be assigned None below
else:
for attr in ["Label", "Species", "Id", "Accession", "Name"]:
if hasattr(freqs, attr):
label = getattr(freqs, attr)
# keep going if the label is empty
if label is not None and label != "":
break
if not label and label != 0:
label = None
if get_color:
try:
color = get_color(freqs)
except:
color = None
else:
if hasattr(freqs, "Color"):
color = freqs.Color
else:
color = None
if get_radius:
try:
radius = get_radius(freqs)
except:
radius = None
else:
if hasattr(freqs, "Radius"):
try:
radius = float(freqs.Radius)
except:
radius = None
else:
radius = None
relevant = Freqs(
{
"A": freqs.get("A", 0),
"C": freqs.get("C", 0),
"G": freqs.get("G", 0),
"U": freqs.get("U", 0) or freqs.get("T", 0),
}
)
relevant.normalize()
return MagePoint((relevant["A"], relevant["C"], relevant["G"]), Label=label, Color=color, Radius=radius)
def test_init(self):
"""BaseFrequency should init as expected"""
self.assertEqual(BaseFrequency('UUUCCCCAG'), \
Freqs('UUUCCCCAG', 'UCAG'))
self.assertEqual(BaseFrequency('TTTCAGG', RNA=False), \
Freqs('TTTCAGG'))
#RnaBases = 'UCAG'
#DnaBases = 'TCAG'
RnaCodons = [i + j + k for i in RnaBases for j in RnaBases for k in RnaBases]
DnaCodons = [i + j + k for i in DnaBases for j in DnaBases for k in DnaBases]
#AminoAcids = 'ACDEFGHIKLMNPQRSTVWY*'
SGC = GeneticCodes[1]
RnaDinucs = [i + j for i in RnaBases for j in RnaBases]
RnaToDna = dict(zip(RnaBases, DnaBases))
DnaToRna = dict(zip(DnaBases, RnaBases))
Bases = RnaBases #by default
Codons = RnaCodons #by default
_equal_bases = Freqs(Bases)
_equal_codons = Freqs(Codons)
_equal_amino_acids = Freqs(AminoAcids[:-1]) #exclude Stop
for i in (_equal_bases, _equal_codons, _equal_amino_acids):
i.normalize()
empty_rna_codons = dict.fromkeys(RnaCodons, 0.0)
empty_dna_codons = dict.fromkeys(DnaCodons, 0.0)
def seq_to_codon_dict(seq, empty_codons=empty_dna_codons):
"""Converts sequence into codon dict."""
leftover = len(seq) % 3
if leftover:
seq += 'A' * (3 - leftover)
result = empty_codons.copy()
