Esempio n. 1
0
	def _trimmed_front(self, match):
		"""Return a trimmed read"""
		read = match.read
		self.lengths_front[match.rstop] += 1
		self.errors_front[match.rstop][match.errors] += 1
		# to remove a front adapter, we need to re-encode the first color following the adapter match
		color_after_adapter = read.sequence[match.rstop:match.rstop + 1]
		if not color_after_adapter:
			# the read is empty
			return read[match.rstop:]
		base_after_adapter = colorspace.DECODE[self.nucleotide_sequence[-1] + color_after_adapter]
		new_first_color = colorspace.ENCODE[read.primer + base_after_adapter]
		seq = new_first_color + read.sequence[(match.rstop + 1):]
		qual = read.qualities[match.rstop:] if read.qualities else None
		return ColorspaceSequence(read.name, seq, qual, read.primer)
Esempio n. 2
0
def test_cs_5p():
	read = ColorspaceSequence("name", b"0123", b"DEFG", b"T")
	adapter = ColorspaceAdapter(b"CG", PREFIX, 0.1)
	cutter = RepeatedAdapterCutter([adapter])
	matches = cutter.find_match(read)
Esempio n. 3
0
 def test_invalid_primer(self):
     ColorspaceSequence(name="name", sequence="K0123", qualities="####")
Esempio n. 4
0
 def test_too_many_qualities_colorspace(self):
     ColorspaceSequence(name="name", sequence="T0123", qualities="#####")
Esempio n. 5
0
def test_cs_5p():
    read = ColorspaceSequence("name", "0123", "DEFG", "T")
    adapter = ColorspaceAdapter("CG", PREFIX, 0.1)
    cutter = AdapterCutter([adapter])
    trimmed_read = cutter(read)
Esempio n. 6
0
def test_cs_5p():
	read = ColorspaceSequence("name", "0123", "DEFG", "T")
	adapter = ColorspaceAdapter("CG", PREFIX, 0.1)
	cutter = AdapterCutter([adapter])
	matches = cutter.find_matches(read)