-def make_parser():
- parser = OptionParser()
- parser.add_option('-o', '--output', help='output fastq file', default=None)
- parser.add_option('-s', '--slice',
- help='specify python slice, e.g. 0:75, 0:-1',
- default=None)
- return parser
-
-def parse_slice(slice_text):
- if slice_text is None or len(slice_text) == 0:
- return slice(None)
-
- slice_data = []
- for element in slice_text.split(':'):
- if len(element) == 0:
- element = None
- else:
- element = int(element)
- slice_data.append(element)
-
- return slice(*slice_data)
-
-def qseq2fastq(destination, qseqs, trim=None):
+def qseq2fastq(destination, qseqs, trim=None, pf=False):