def test_dustscore_calculation():
'It calculates the dust score'
seqs = ['TTTTTTTTTTTTTTTTTTTTTTTTTTTT', 'TATATATATATATATATATATATATATA',
'GAAGAAGAAGAAGAAGAAGAAGAAGAAG', 'AACTGCAGTCGATGCTGATTCGATCGAT',
'AACTGAAAAAAAATTTTTTTAAAAAAAA']
# short sequences
scores = [100, 48, 30.76, 4.31, 23.38]
scoresx3 = [100, 48.68, 28.65, 5.62, 27.53]
scoresx4 = [100, 48.55, 28.25, 5.79, 28.00]
for seq, score, scorex3, scorex4 in zip(seqs, scores, scoresx3,
scoresx4):
seqrec = SeqRecord(Seq(seq))
seqrec = SeqWrapper(SEQRECORD, seqrec, None)
assert calculate_dust_score(seqrec) - score < 0.01
seqrec = SeqRecord(Seq(seq * 3))
seqrec = SeqWrapper(SEQRECORD, seqrec, None)
assert calculate_dust_score(seqrec) - scorex3 < 0.01
seqrec = SeqRecord(Seq(seq * 4))
seqrec = SeqWrapper(SEQRECORD, seqrec, None)
assert calculate_dust_score(seqrec) - scorex4 < 0.01
def test_dustscore_calculation():
'It calculates the dust score'
seqs = ['TTTTTTTTTTTTTTTTTTTTTTTTTTTT', 'TATATATATATATATATATATATATATA',
'GAAGAAGAAGAAGAAGAAGAAGAAGAAG', 'AACTGCAGTCGATGCTGATTCGATCGAT',
'AACTGAAAAAAAATTTTTTTAAAAAAAA']
# short sequences
scores = [100, 48, 30.76, 4.31, 23.38]
scoresx3 = [100, 48.68, 28.65, 5.62, 27.53]
scoresx4 = [100, 48.55, 28.25, 5.79, 28.00]
for seq, score, scorex3, scorex4 in zip(seqs, scores, scoresx3,
scoresx4):
seqrec = SeqRecord(Seq(seq))
seqrec = SeqWrapper(SEQRECORD, seqrec, None)
assert calculate_dust_score(seqrec) - score < 0.01
seqrec = SeqRecord(Seq(seq * 3))
seqrec = SeqWrapper(SEQRECORD, seqrec, None)
assert calculate_dust_score(seqrec) - scorex3 < 0.01
seqrec = SeqRecord(Seq(seq * 4))
seqrec = SeqWrapper(SEQRECORD, seqrec, None)
assert calculate_dust_score(seqrec) - scorex4 < 0.01
def __call__(self, snv):
self._clean_filter(snv)
# we have to make all the posible conbinations
chrom = snv.chrom
last_chrom = self._last_chrom
if last_chrom is not None and chrom == self._last_chrom[0]:
ref = last_chrom[1]
else:
ref = self.ref_index[snv.chrom]
self._last_chrom = chrom, ref
start, end = calculate_window(snv.pos, snv.end, self.window, len(ref))
snv_win_seq = SeqWrapper(SEQRECORD, ref[start:end], None)
score = calculate_dust_score(snv_win_seq)
if score > self.threshold:
snv.add_filter(self.name)
self._scores.append(score)
if self.return_modified_snv:
return snv
def __call__(self, snv):
self._clean_filter(snv)
# we have to make all the posible conbinations
chrom = snv.chrom
last_chrom = self._last_chrom
if last_chrom is not None and chrom == self._last_chrom[0]:
ref = last_chrom[1]
else:
ref = self.ref_index[snv.chrom]
self._last_chrom = chrom, ref
start, end = calculate_window(snv.pos, snv.end, self.window, len(ref))
snv_win_seq = SeqWrapper(SEQRECORD, ref[start:end], None)
score = calculate_dust_score(snv_win_seq)
if score > self.threshold:
snv.add_filter(self.name)
self._scores.append(score)
if self.return_modified_snv:
return snv
def _do_check(self, seq):
threshold = self._threshold
dustscore = calculate_dust_score(seq)
return True if dustscore < threshold else False
def _do_check(self, seq):
threshold = self._threshold
dustscore = calculate_dust_score(seq)
return True if dustscore < threshold else False
