How to use the cutadapt.parser.AdapterSpecification function in cutadapt
To help you get started, we’ve selected a few cutadapt examples, based on popular ways it is used in public projects.
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marcelm / cutadapt / tests / test_parser.py View on Github 
def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')def test_expand_braces():
expand_braces = AdapterSpecification.expand_braces
assert expand_braces('') == ''
assert expand_braces('A') == 'A'
assert expand_braces('A{0}') == ''
assert expand_braces('A{1}') == 'A'
assert expand_braces('A{2}') == 'AA'
assert expand_braces('A{2}C') == 'AAC'
assert expand_braces('ACGTN{3}TGACCC') == 'ACGTNNNTGACCC'
assert expand_braces('ACGTN{10}TGACCC') == 'ACGTNNNNNNNNNNTGACCC'
assert expand_braces('ACGTN{3}TGA{4}CCC') == 'ACGTNNNTGAAAACCC'
assert expand_braces('ACGTN{0}TGA{4}CCC') == 'ACGTTGAAAACCC'def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')def test_parse_not_linked():
p = AdapterSpecification.parse
assert p('A', 'front') == AdapterSpecification(None, None, 'A', {}, 'front')
assert p('A', 'back') == AdapterSpecification(None, None, 'A', {}, 'back')
assert p('A', 'anywhere') == AdapterSpecification(None, None, 'A', {}, 'anywhere')
assert p('^A', 'front') == AdapterSpecification(None, 'anchored', 'A', {}, 'front')
assert p('XXXA', 'front') == AdapterSpecification(None, 'noninternal', 'A', {}, 'front')
assert p('A$', 'back') == AdapterSpecification(None, 'anchored', 'A', {}, 'back')
assert p('AXXXX', 'back') == AdapterSpecification(None, 'noninternal', 'A', {}, 'back')
assert p('a_name=ADAPT', 'front') == AdapterSpecification('a_name', None, 'ADAPT', {}, 'front')cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Package Health Score
83 / 100Popular cutadapt functions
- cutadapt.__main__.main
- cutadapt.__main__.parse_lengths
- cutadapt.adapters.BackAdapter
- cutadapt.adapters.PrefixAdapter
- cutadapt.adapters.warn_duplicate_adapters
- cutadapt.align.Aligner
- cutadapt.colorspace.encode
- cutadapt.modifiers.AdapterCutter
- cutadapt.modifiers.ModificationInfo
- cutadapt.modifiers.QualityTrimmer
- cutadapt.modifiers.Shortener
- cutadapt.modifiers.UnconditionalCutter
- cutadapt.parser.AdapterParser
- cutadapt.parser.AdapterSpecification
- cutadapt.seqio.FastaReader
- cutadapt.seqio.FastaWriter
- cutadapt.seqio.FastqReader
- cutadapt.seqio.find_fastq_record_end
- cutadapt.seqio.open
- cutadapt.seqio.Sequence