def test_rolling_window(self):
'We get the items along a rolling window'
# with series
serie = '12345'
assert [''.join(win) for win in rolling_window(serie, 3)] == ['123',
'234', '345']
assert not [''.join(win) for win in rolling_window(serie, 6)]
assert [''.join(w) for w in rolling_window(serie, 5)] == ['12345']
# with iterator
iterator = iter(serie)
assert [''.join(win) for win in rolling_window(iterator, 3)] == ['123',
'234', '345']
iterator = iter(serie)
assert not [''.join(win) for win in rolling_window(iterator, 6)]
iterator = iter(serie)
assert [''.join(w) for w in rolling_window(iterator, 5)] == ['12345']
# with step
series = ['1234567890', '123456789', '12345678', '1234567']
expected = [['1234', '3456', '5678', '7890'], ['1234', '3456', '5678'],
['1234', '3456', '5678'], ['1234', '3456']]
for serie, exp in zip(series, expected):
wins1 = [''.join(win) for win in rolling_window(serie, 4, 2)]
assert wins1 == exp
iterator = iter(serie)
wins2 = [''.join(win) for win in rolling_window(iterator, 4, 2)]
assert wins1 == wins2
def test_rolling_window(self):
'We get the items along a rolling window'
# with series
serie = '12345'
assert [''.join(win) for win in rolling_window(serie, 3)] == ['123',
'234', '345']
assert not [''.join(win) for win in rolling_window(serie, 6)]
assert [''.join(w) for w in rolling_window(serie, 5)] == ['12345']
# with iterator
iterator = iter(serie)
assert [''.join(win) for win in rolling_window(iterator, 3)] == ['123',
'234', '345']
iterator = iter(serie)
assert not [''.join(win) for win in rolling_window(iterator, 6)]
iterator = iter(serie)
assert [''.join(w) for w in rolling_window(iterator, 5)] == ['12345']
# with step
series = ['1234567890', '123456789', '12345678', '1234567']
expected = [['1234', '3456', '5678', '7890'], ['1234', '3456', '5678'],
['1234', '3456', '5678'], ['1234', '3456']]
for serie, exp in zip(series, expected):
wins1 = [''.join(win) for win in rolling_window(serie, 4, 2)]
assert wins1 == exp
iterator = iter(serie)
wins2 = [''.join(win) for win in rolling_window(iterator, 4, 2)]
assert wins1 == wins2
def _calculate_rawscore(string):
'It returns a non-normalized dustscore'
triplet_counts = Counter()
for triplet in rolling_window(string, 3):
# It should do something with non ATCG, but we sacrifice purity for
# speed. Maybe we should reconsider this
triplet_counts[triplet.upper()] += 1
return sum(tc * (tc - 1) * 0.5 for tc in triplet_counts.viewvalues())
def _get_bad_quality_segments(quals,
window,
threshold,
trim_left=True,
trim_right=True):
'''It returns the regions with quality above the threshold.
The algorithm is similar to the one used by qclip in Staden.
'''
# do window quality means
mean = lambda l: float(sum(l)) / len(l) if len(l) > 0 else float('nan')
wquals = [mean(win_quals) for win_quals in rolling_window(quals, window)]
if not wquals:
return [(0, len(quals) - 1)]
index_max, max_val = max(enumerate(wquals), key=itemgetter(1))
if max_val < threshold:
return [(0, len(quals) - 1)]
if trim_left:
wleft_index = 0
for wleft_index in range(index_max - 1, -1, -1):
if wquals[wleft_index] < threshold:
wleft_index += 1
break
else:
wleft_index = 0
if trim_right:
wright_index = index_max
for wright_index in range(index_max, len(wquals)):
if wquals[wright_index] < threshold:
wright_index -= 1
break
else:
wright_index = len(wquals) - 1
left = wleft_index
right = wright_index + window - 1
segments = []
if left:
segments.append((0, left - 1))
if right < len(quals) - 1:
segments.append((right + 1, len(quals) - 1))
if not segments:
return None
return segments
def _get_bad_quality_segments(quals, window, threshold, trim_left=True,
trim_right=True):
'''It returns the regions with quality above the threshold.
The algorithm is similar to the one used by qclip in Staden.
'''
# do window quality means
mean = lambda l: float(sum(l)) / len(l) if len(l) > 0 else float('nan')
wquals = [mean(win_quals) for win_quals in rolling_window(quals, window)]
if not wquals:
return [(0, len(quals) - 1)]
index_max, max_val = max(enumerate(wquals), key=itemgetter(1))
if max_val < threshold:
return [(0, len(quals) - 1)]
if trim_left:
wleft_index = 0
for wleft_index in range(index_max - 1, -1, -1):
if wquals[wleft_index] < threshold:
wleft_index += 1
break
else:
wleft_index = 0
if trim_right:
wright_index = index_max
for wright_index in range(index_max, len(wquals)):
if wquals[wright_index] < threshold:
wright_index -= 1
break
else:
wright_index = len(wquals) - 1
left = wleft_index
right = wright_index + window - 1
segments = []
if left:
segments.append((0, left - 1))
if right < len(quals) - 1:
segments.append((right + 1, len(quals) - 1))
if not segments:
return None
return segments
def calculate_dust_score(seq):
'''It returns the dust score.
From: "A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA
Sequences"
doi:10.1089/cmb.2006.13.1028
and re-implemented from PRINSEQ
'''
seq = get_str_seq(seq)
length = len(seq)
if length == 3:
return 0
if length <= 5:
return None
windowsize = get_setting('DUST_WINDOWSIZE')
windowstep = get_setting('DUST_WINDOWSTEP')
dustscores = []
if length > windowsize:
windows = 0
for seq_in_win in rolling_window(seq, windowsize, windowstep):
score = _calculate_rawscore(seq_in_win)
dustscores.append(score / (windowsize - 2))
windows += 1
remaining_seq = seq[windows * windowstep:]
else:
remaining_seq = seq
if remaining_seq > 5:
length = len(remaining_seq)
score = _calculate_rawscore(remaining_seq)
dustscore = score / (length - 3) * (windowsize - 2) / (length - 2)
dustscores.append(dustscore)
# max score should be 100 not 31
dustscore = sum(dustscores) / len(dustscores) * 100 / 31
return dustscore
def test_rolling_window(self):
'We get the items along a rolling window'
#with series
serie = '12345'
assert [''.join(win) for win in rolling_window(serie, 3)] == ['123',
'234', '345']
assert not [''.join(win) for win in rolling_window(serie, 6)]
assert [''.join(w) for w in rolling_window(serie, 5)] == ['12345']
#with iterator
iterator = iter(serie)
assert [''.join(win) for win in rolling_window(iterator, 3)] == ['123',
'234', '345']
iterator = iter(serie)
assert not [''.join(win) for win in rolling_window(iterator, 6)]
iterator = iter(serie)
assert [''.join(w) for w in rolling_window(iterator, 5)] == ['12345']
def count_seq(self, serie):
'It adds the kmers of the given iterable/serie'
for kmer in rolling_window(serie, self._kmer_size):
self._counter[kmer] += 1
def count_seq(self, serie):
'It adds the kmers of the given iterable/serie'
for kmer in rolling_window(serie, self._kmer_size):
self._counter[kmer] += 1
