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 SAP.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 SAP.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 SAP.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)
def _fastq_solexa_convert_qual(in_handle, out_handle, alphabet=None):
"""Fast Solexa FASTQ to QUAL conversion (PRIVATE)."""
from SAP.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)
