Example #1
0
 def annotate(self, R1, R2, pct, frac):
     ids = utils.parse_read_ids(R1)
     return [(id, True) for id in ids]
Example #2
0
 def annotate(self, R1, R2, pct, frac):
     sam_file, stderr_file = self._run(R1, R2)
     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]
Example #3
0
 def annotate(self, R1, R2):
     ids = utils.parse_read_ids(R1)
     return [(id, False) for id in ids]
Example #4
0
 def annotate(self, R1, R2, pct, frac):
     ids = utils.parse_read_ids(R1)
     return [
         (id, True if random.random() <= self.fraction_human else False)
         for id in ids]
Example #5
0
 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]
Example #6
0
 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]
Example #7
0
 def annotate(self, R1, R2, pct, frac, output_dir):
     ids = utils.parse_read_ids(R1)
     return [(id, True) for id in ids]
Example #8
0
 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]
Example #9
0
 def annotate(self, R1, R2, pct, frac):
     ids = utils.parse_read_ids(R1)
     return [(id, False) for id in ids]