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#cython: language_level=3
cimport cython
from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN
from obitools3.utils cimport bytes2str, str2bytes, tobytes
# TODO quality offset option?
cdef class FastqFormat:
def __init__(self, list tags=[], bint printNAKeys=False, bytes NAString=b"NA", bint NAIntTo0=False):
self.headerFormatter = HeaderFormat("fastq",
tags=tags,
printNAKeys=printNAKeys,
NAString=NAString,
NAIntTo0=NAIntTo0)
@cython.boundscheck(False)
def __call__(self, object data):
cdef bytes quality
quality = None
if hasattr(data, "quality_bytes"):
quality = data.quality_bytes
elif hasattr(data, "quality"):
quality = tobytes(data.quality)
if quality is None:
raise AttributeError("No quality when exporting to fastq") # TODO discuss
return self.headerFormatter(data) + b"\n" + data[NUC_SEQUENCE_COLUMN] + b"\n+\n" + quality
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