Esempi in Python per _get_nth_sequence

Esempio n. 1

File: fastq.py Progetto: johnchase/scikit-bio

def _fastq_to_protein_sequence(fh, variant=None, phred_offset=None, seq_num=1,
                               **kwargs):
    return _get_nth_sequence(
        _fastq_to_generator(fh, variant=variant, phred_offset=phred_offset,
                            constructor=Protein,
                            **kwargs),
        seq_num)

Esempio n. 2

File: fastq.py Progetto: jessdwitch/scikit-bio

def _fastq_to_protein_sequence(fh, variant=None, phred_offset=None, seq_num=1,
                               **kwargs):
    return _get_nth_sequence(
        _fastq_to_generator(fh, variant=variant, phred_offset=phred_offset,
                            constructor=Protein,
                            **kwargs),
        seq_num)

Esempio n. 3

File: qseq.py Progetto: johnchase/scikit-bio

def _qseq_to_protein_sequence(fh, seq_num=1,
                              phred_offset=_default_phred_offset,
                              variant=_default_variant, **kwargs):
    return _get_nth_sequence(_qseq_to_generator(fh, filter=False,
                             phred_offset=phred_offset, variant=variant,
                             constructor=Protein, **kwargs),
                             seq_num)

Esempio n. 4

File: qseq.py Progetto: bctaylor/scikit-bio

def _qseq_to_protein_sequence(fh, seq_num=1,
                              phred_offset=_default_phred_offset,
                              variant=_default_variant):
    return _get_nth_sequence(_qseq_to_generator(fh, filter=False,
                             phred_offset=phred_offset, variant=variant,
                             constructor=partial(Protein, validate=False)),
                             seq_num)

Esempio n. 5

File: fastq.py Progetto: squarednob/scikit-bio

def _fastq_to_biological_sequence(fh,
                                  variant=None,
                                  phred_offset=None,
                                  seq_num=1):
    return _get_nth_sequence(
        _fastq_to_generator(fh,
                            variant=variant,
                            phred_offset=phred_offset,
                            constructor=BiologicalSequence), seq_num)

Esempio n. 6

File: fastq.py Progetto: squarednob/scikit-bio

def _fastq_to_nucleotide_sequence(fh,
                                  variant=None,
                                  phred_offset=None,
                                  seq_num=1):
    return _get_nth_sequence(
        _fastq_to_generator(fh,
                            variant=variant,
                            phred_offset=phred_offset,
                            constructor=NucleotideSequence), seq_num)

Esempio n. 7

File: qseq.py Progetto: jessdwitch/scikit-bio

def _qseq_to_biological_sequence(fh,
                                 seq_num=1,
                                 phred_offset=_default_phred_offset,
                                 variant=_default_variant):
    return _get_nth_sequence(
        _qseq_to_generator(fh,
                           filter=False,
                           phred_offset=phred_offset,
                           variant=variant,
                           constructor=Sequence), seq_num)

Esempio n. 8

File: qseq.py Progetto: jessdwitch/scikit-bio

def _qseq_to_protein_sequence(fh,
                              seq_num=1,
                              phred_offset=_default_phred_offset,
                              variant=_default_variant,
                              **kwargs):
    return _get_nth_sequence(
        _qseq_to_generator(fh,
                           filter=False,
                           phred_offset=phred_offset,
                           variant=variant,
                           constructor=Protein,
                           **kwargs), seq_num)

Esempio n. 9

File: fastq.py Progetto: 7924102/scikit-bio

def _fastq_to_protein_sequence(fh, variant=None, phred_offset=None, seq_num=1):
    return _get_nth_sequence(
        _fastq_to_generator(fh, variant=variant, phred_offset=phred_offset,
                            constructor=partial(Protein, validate=False)),
        seq_num)

Esempio n. 10

File: fastq.py Progetto: 7924102/scikit-bio

def _fastq_to_biological_sequence(fh, variant=None, phred_offset=None,
                                  seq_num=1):
    return _get_nth_sequence(
        _fastq_to_generator(fh, variant=variant, phred_offset=phred_offset,
                            constructor=Sequence),
        seq_num)

Esempio n. 11

def _fasta_to_protein_sequence(fh, qual=FileSentinel, seq_num=1, **kwargs):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual, constructor=Protein, **kwargs),
        seq_num)

Esempio n. 12

def _fasta_to_biological_sequence(fh, qual=FileSentinel, seq_num=1):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual, constructor=Sequence), seq_num)

Esempio n. 13

File: fasta.py Progetto: AndreaEdwards/scikit-bio

def _fasta_to_nucleotide_sequence(fh, qual=FileSentinel, seq_num=1):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual, constructor=NucleotideSequence),
        seq_num)

Esempio n. 14

File: test_base.py Progetto: jessdwitch/scikit-bio

    def test_seq_num_too_big(self):
        with self.assertRaises(ValueError) as cm:
            _get_nth_sequence(self.gen, 6)

        self.assertIn('end of file', str(cm.exception))
        self.assertIn('6th', str(cm.exception))

Esempio n. 15

File: test_base.py Progetto: 7924102/scikit-bio

 def test_seq_num_just_right(self):
     value = _get_nth_sequence(self.gen, 3)
     self.assertEqual(value, 'goldilocks: 3')

Esempio n. 16

File: test_base.py Progetto: 7924102/scikit-bio

    def test_seq_num_too_small(self):
        with self.assertRaises(ValueError) as cm:
            _get_nth_sequence(self.gen, 0)

        self.assertIn('between 1 and', str(cm.exception))
        self.assertIn('0', str(cm.exception))

Esempio n. 17

File: qseq.py Progetto: bctaylor/scikit-bio

def _qseq_to_biological_sequence(fh, seq_num=1,
                                 phred_offset=_default_phred_offset,
                                 variant=_default_variant):
    return _get_nth_sequence(_qseq_to_generator(fh, filter=False,
                             phred_offset=phred_offset, variant=variant,
                             constructor=Sequence), seq_num)

Esempio n. 18

File: fasta.py Progetto: AndreaEdwards/scikit-bio

def _fasta_to_protein_sequence(fh, qual=FileSentinel, seq_num=1):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual, constructor=ProteinSequence),
        seq_num)

Esempio n. 19

File: fasta.py Progetto: bctaylor/scikit-bio

def _fasta_to_protein_sequence(fh, qual=FileSentinel, seq_num=1):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual,
                            constructor=partial(Protein, validate=False)),
        seq_num)

Esempio n. 20

File: fasta.py Progetto: bctaylor/scikit-bio

def _fasta_to_biological_sequence(fh, qual=FileSentinel, seq_num=1):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual, constructor=Sequence),
        seq_num)

Esempio n. 21

File: test_base.py Progetto: 7924102/scikit-bio

    def test_seq_num_too_big(self):
        with self.assertRaises(ValueError) as cm:
            _get_nth_sequence(self.gen, 6)

        self.assertIn('end of file', str(cm.exception))
        self.assertIn('6th', str(cm.exception))

Esempio n. 22

File: fastq.py Progetto: Kleptobismol/scikit-bio

def _fastq_to_nucleotide_sequence(fh, variant=None, phred_offset=None,
                                  seq_num=1):
    return _get_nth_sequence(
        _fastq_to_generator(fh, variant=variant, phred_offset=phred_offset,
                            constructor=NucleotideSequence),
        seq_num)

Esempio n. 23

File: test_base.py Progetto: jessdwitch/scikit-bio

    def test_seq_num_too_small(self):
        with self.assertRaises(ValueError) as cm:
            _get_nth_sequence(self.gen, 0)

        self.assertIn('between 1 and', str(cm.exception))
        self.assertIn('0', str(cm.exception))

Esempio n. 24

File: fasta.py Progetto: Achuth17/scikit-bio

def _fasta_to_rna_sequence(fh, qual=FileSentinel, seq_num=1, **kwargs):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual,
                            constructor=RNA, **kwargs),
        seq_num)

Esempio n. 25

File: test_base.py Progetto: jessdwitch/scikit-bio

 def test_seq_num_just_right(self):
     value = _get_nth_sequence(self.gen, 3)
     self.assertEqual(value, 'goldilocks: 3')

Esempio n. 26

File: fasta.py Progetto: squarednob/scikit-bio

def _fasta_to_nucleotide_sequence(fh, qual=FileSentinel, seq_num=1):
    return _get_nth_sequence(
        _fasta_to_generator(fh, qual=qual, constructor=NucleotideSequence),
        seq_num)