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 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_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 Bio.SeqIO.QualityIO import solexa_quality_from_phred
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 Bio.SeqIO.QualityIO import solexa_quality_from_phred
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 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")
