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