How to use the dnaio.Sequence function in dnaio
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marcelm / cutadapt / tests / test_utils.py View on Github 
def test_reverse_complemented_sequence():
s = dnaio.Sequence("the_name", "ACGTTTGA", "B>%%BB5#")
assert reverse_complemented_sequence(s) == dnaio.Sequence("the_name", "TCAAACGT", "#5BB%%>B")
s = dnaio.Sequence("the_name", "ACGTTTGA")
assert reverse_complemented_sequence(s) == dnaio.Sequence("the_name", "TCAAACGT")def test_reverse_complemented_sequence():
s = dnaio.Sequence("the_name", "ACGTTTGA", "B>%%BB5#")
assert reverse_complemented_sequence(s) == dnaio.Sequence("the_name", "TCAAACGT", "#5BB%%>B")
s = dnaio.Sequence("the_name", "ACGTTTGA")
assert reverse_complemented_sequence(s) == dnaio.Sequence("the_name", "TCAAACGT")def test_nend_trimmer():
trimmer = NEndTrimmer()
seqs = ['NNNNAAACCTTGGNNN', 'NNNNAAACNNNCTTGGNNN', 'NNNNNN']
trims = ['AAACCTTGG', 'AAACNNNCTTGG', '']
for seq, trimmed in zip(seqs, trims):
_seq = Sequence('read1', seq, qualities='#'*len(seq))
_trimmed = Sequence('read1', trimmed, qualities='#'*len(trimmed))
assert trimmer(_seq, ModificationInfo(_seq)) == _trimmeddef test_nextseq_trim():
s = Sequence('n', '', '')
assert nextseq_trim_index(s, cutoff=22) == 0
s = Sequence(
'n',
'TCTCGTATGCCGTCTTATGCTTGAAAAAAAAAAGGGGGGGGGGGGGGGGGNNNNNNNNNNNGGNGG',
'AA//EAEE//A6///E//A//EA/EEEEEEAEA//EEEEEEEEEEEEEEE###########EE#EA'
)
assert nextseq_trim_index(s, cutoff=22) == 33def test_linked_adapter():
front_adapter = PrefixAdapter('AAAA', min_overlap=4)
back_adapter = BackAdapter('TTTT', min_overlap=3)
linked_adapter = LinkedAdapter(
front_adapter, back_adapter, front_required=True, back_required=False, name='name')
assert linked_adapter.front_adapter.min_overlap == 4
assert linked_adapter.back_adapter.min_overlap == 3
read = Sequence(name='seq', sequence='AAAACCCCCTTTT')
trimmed = linked_adapter.match_to(read.sequence).trimmed(read)
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'def test_statistics():
read = Sequence('name', 'AAAACCCCAAAA')
adapters = [BackAdapter("CCCC", max_error_rate=0.1)]
cutter = AdapterCutter(adapters, times=3)
cutter(read, ModificationInfo(read))
# TODO make this a lot simpler
trimmed_bp = 0
for adapter in adapters:
for d in (cutter.adapter_statistics[adapter].front.lengths,
cutter.adapter_statistics[adapter].back.lengths):
trimmed_bp += sum(seqlen * count for (seqlen, count) in d.items())
assert trimmed_bp <= len(read), trimmed_bpdef test_shortener():
read = Sequence('read1', 'ACGTTTACGTA', '##456789###')
shortener = Shortener(0)
assert shortener(read, ModificationInfo(read)) == Sequence('read1', '', '')
shortener = Shortener(1)
assert shortener(read, ModificationInfo(read)) == Sequence('read1', 'A', '#')
shortener = Shortener(5)
assert shortener(read, ModificationInfo(read)) == Sequence('read1', 'ACGTT', '##456')
shortener = Shortener(100)
assert shortener(read, ModificationInfo(read)) == readdef test_reverse_complemented_sequence():
s = dnaio.Sequence("the_name", "ACGTTTGA", "B>%%BB5#")
assert reverse_complemented_sequence(s) == dnaio.Sequence("the_name", "TCAAACGT", "#5BB%%>B")
s = dnaio.Sequence("the_name", "ACGTTTGA")
assert reverse_complemented_sequence(s) == dnaio.Sequence("the_name", "TCAAACGT")def test_anywhere_parameter_front():
parser = AdapterParser(max_error_rate=0.2, min_overlap=4, read_wildcards=False,
adapter_wildcards=False, indels=True)
adapter = list(parser.parse('CTGAAGTGAAGTACACGGTT;anywhere', 'front'))[0]
assert isinstance(adapter, FrontAdapter)
assert adapter._force_anywhere
# TODO move the rest to a separate test
read = Sequence('foo1', 'AAAAAAAAAACTGAAGTGAA')
from cutadapt.modifiers import AdapterCutter
cutter = AdapterCutter([adapter])
trimmed_read = cutter(read, ModificationInfo(read))
assert trimmed_read.sequence == ''def reverse_complemented_sequence(sequence: dnaio.Sequence):
if sequence.qualities is None:
qualities = None
else:
qualities = sequence.qualities[::-1]
return dnaio.Sequence(sequence.name, reverse_complement(sequence.sequence), qualities)dnaio
Read and write FASTA and FASTQ files efficiently
