def _fastq_illumina_convert_fastq_solexa(in_handle, out_handle, alphabet=None):
"""Fast Illumina 1.3+ FASTQ to Solexa 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 solexa_quality_from_phred
trunc_char = chr(1)
mapping = "".join([chr(0) for ascii in range(0, 64)] + [
chr(64 + int(round(solexa_quality_from_phred(q))))
for q in range(0, 62 + 1)
] + [chr(0) for ascii in range(127, 256)])
assert len(mapping) == 256
return _fastq_generic(in_handle, out_handle, mapping)
def _fastq_illumina_convert_fastq_solexa(in_handle, out_handle, alphabet=None):
"""Fast Illumina 1.3+ FASTQ to Solexa 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 solexa_quality_from_phred
trunc_char = chr(1)
mapping = "".join([chr(0) for ascii in range(0, 64)]
+ [chr(64 + int(round(solexa_quality_from_phred(q))))
for q in range(0, 62 + 1)]
+ [chr(0) for ascii in range(127, 256)])
assert len(mapping) == 256
return _fastq_generic(in_handle, out_handle, mapping)
def _fastq_sanger_convert_fastq_solexa(in_handle, out_handle, alphabet=None):
"""Fast Sanger FASTQ to Solexa FASTQ conversion (PRIVATE).
Avoids creating SeqRecord and Seq objects in order to speed up this
conversion. Will issue a warning if the scores had to be truncated at 62
(maximum possible in the Solexa FASTQ format)
"""
#Map unexpected chars to null
from SAP.Bio.SeqIO.QualityIO import solexa_quality_from_phred
trunc_char = chr(1)
mapping = "".join([chr(0) for ascii in range(0, 33)]
+ [chr(64 + int(round(solexa_quality_from_phred(q))))
for q in range(0, 62 + 1)]
+ [trunc_char for ascii in range(96, 127)]
+ [chr(0) for ascii in range(127, 256)])
assert len(mapping) == 256
return _fastq_generic2(in_handle, out_handle, mapping, trunc_char,
"Data loss - max Solexa quality 62 in Solexa FASTQ")
def _fastq_sanger_convert_fastq_solexa(in_handle, out_handle, alphabet=None):
"""Fast Sanger FASTQ to Solexa FASTQ conversion (PRIVATE).
Avoids creating SeqRecord and Seq objects in order to speed up this
conversion. Will issue a warning if the scores had to be truncated at 62
(maximum possible in the Solexa FASTQ format)
"""
#Map unexpected chars to null
from SAP.Bio.SeqIO.QualityIO import solexa_quality_from_phred
trunc_char = chr(1)
mapping = "".join([chr(0) for ascii in range(0, 33)] + [
chr(64 + int(round(solexa_quality_from_phred(q))))
for q in range(0, 62 + 1)
] + [trunc_char
for ascii in range(96, 127)] + [chr(0) for ascii in range(127, 256)])
assert len(mapping) == 256
return _fastq_generic2(
in_handle, out_handle, mapping, trunc_char,
"Data loss - max Solexa quality 62 in Solexa FASTQ")