def annotate(self, R1, R2, pct, frac, output_dir):
mapped = self._get_mapped_reads(self.sam_fp, pct, frac)
ids = utils.parse_read_ids(R1)
return [(id, True if id in mapped else False) for id in ids]
def annotate(self, R1, R2, pct, frac, output_dir):
sam_file, stderr_file = self._run(R1, R2, output_dir)
mapped = self._get_mapped_reads(sam_file.name, pct, frac)
ids = utils.parse_read_ids(R1)
return [(id, True if id in mapped else False) for id in ids]
def annotate(self, R1, R2, pct, frac, output_dir):
ids = utils.parse_read_ids(R1)
return [
(id, True if random.random() <= self.fraction_human else False)
for id in ids]
def annotate(self, R1, R2, pct, frac, output_dir):
ids = utils.parse_read_ids(R1)
return [(id, True) for id in ids]
def test_ids(self):
ids = utils.parse_read_ids(self.fastq.name)
self.assertEqual(len(ids), 3)
self.assertTrue("1" in ids)
self.assertTrue("2" in ids)
self.assertTrue("3" in ids)
def annotate(self, R1, R2, pct, frac, output_dir):
sam_file, stderr_file = self._run(R1, R2, output_dir)
mapped = self._get_mapped_reads(sam_file.name, pct, frac)
ids = utils.parse_read_ids(R1)
return [(id, True if id in mapped else False) for id in ids]
def annotate(self, R1, R2, pct, frac, output_dir):
mapped = self._get_mapped_reads(self.sam_fp, pct, frac)
ids = utils.parse_read_ids(R1)
return [(id, True if id in mapped else False) for id in ids]
def annotate(self, R1, R2, pct, frac, output_dir):
ids = utils.parse_read_ids(R1)
return [(id, True) for id in ids]
def annotate(self, R1, R2, pct, frac, output_dir):
ids = utils.parse_read_ids(R1)
return [(id, True if random.random() <= self.fraction_human else False)
for id in ids]
