def _fastq_solexa_convert_qual(in_handle, out_handle, alphabet=None): """Fast Solexa FASTQ to QUAL conversion (PRIVATE).""" from Bio.SeqIO.QualityIO import phred_quality_from_solexa mapping = { chr(q + 64): str(int(round(phred_quality_from_solexa(q)))) for q in range(-5, 62 + 1) } return _fastq_convert_qual(in_handle, out_handle, mapping)
def _fastq_solexa_convert_fastq_illumina(in_handle, out_handle, alphabet=None): """Fast Solexa FASTQ to Illumina 1.3+ FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. """ #Map unexpected chars to null from Bio.SeqIO.QualityIO import phred_quality_from_solexa mapping = "".join([chr(0) for ascii in range(0, 59)] \ +[chr(64+int(round(phred_quality_from_solexa(q)))) \ for q in range(-5, 62+1)]\ +[chr(0) for ascii in range(127, 256)]) assert len(mapping)==256 return _fastq_generic(in_handle, out_handle, mapping)
def _fastq_solexa_convert_fastq_illumina(in_handle, out_handle, alphabet=None): """Fast Solexa FASTQ to Illumina 1.3+ FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. """ #Map unexpected chars to null from Bio.SeqIO.QualityIO import phred_quality_from_solexa mapping = "".join([chr(0) for ascii in range(0,59)] \ +[chr(64+int(round(phred_quality_from_solexa(q)))) \ for q in range(-5,62+1)]\ +[chr(0) for ascii in range(127,256)]) assert len(mapping) == 256 return _fastq_generic(in_handle, out_handle, mapping)
def _fastq_solexa_convert_qual(in_handle, out_handle, alphabet=None): """Fast Solexa FASTQ to QUAL conversion (PRIVATE).""" from Bio.SeqIO.QualityIO import phred_quality_from_solexa mapping = dict((chr(q+64), str(int(round(phred_quality_from_solexa(q))))) \ for q in range(-5,62+1)) return _fastq_convert_qual(in_handle, out_handle, mapping)