diff --git a/python/obitools3/parsers/universal.pyx b/python/obitools3/parsers/universal.pyx index 280a1e2..b92a4cf 100644 --- a/python/obitools3/parsers/universal.pyx +++ b/python/obitools3/parsers/universal.pyx @@ -1,7 +1,10 @@ +#cython: language_level=3 + import re from obitools3.parsers.fasta import fastaNucIterator from obitools3.parsers.fastq import fastqIterator + oligore = re.compile("^[ACGTRYSWKMBDHVN]+$",re.I) tagre = re.compile("^([ACGTRYSWKMBDHVN]+|-)(:([ACGTRYSWKMBDHVN]+)|-)?$",re.I) @@ -21,14 +24,14 @@ def entryIteratorFactory(lineiterator, only=None, bytes seqtype=b'nuc', int qualityoffset=32, - bool noquality=False, - bool skiperror=True, - bool header=False, + bint noquality=False, + bint skiperror=True, + bint header=False, bytes sep=None, bytes dec=b'.', bytes nastring=b"NA", - bool stripwhite=True, - bool blanklineskip=True, + bint stripwhite=True, + bint blanklineskip=True, bytes commentchar=b"#", int buffersize=100000000): @@ -70,7 +73,7 @@ def entryIteratorFactory(lineiterator, Nuc_Seq) else: raise NotImplementedError() - elif format=b'fastq': + elif format==b'fastq': return (fastqIterator(lineiterator, skip,only, qualityoffset,