Open Crispy13 opened 8 months ago
test code:
import sys import timeit from tqdm.auto import tqdm import pysam def main(): samfile = pysam.AlignmentFile( "my.bam", "rb" ) qns = [] qa = qns.append # pbar = tqdm() for pileupcolumn in samfile.pileup("chr1", 11108234-1, 11108234, truncate=True): for p in pileupcolumn.pileups: qn = p.alignment.query_name qa(qn) # pbar.update(1) if __name__ == '__main__': print(f"{sys.version=}") print(f"{pysam.__version__=}") print(timeit.repeat(main, number = 100, repeat=5))
Results:
sys.version='3.9.9 | packaged by conda-forge | (main, Dec 20 2021, 02:41:03) \n[GCC 9.4.0]' pysam.__version__='0.16.0.1' [3.182755395071581, 3.193303174106404, 3.189940463984385, 3.197926699882373, 3.1971522108651698] sys.version='3.9.9 | packaged by conda-forge | (main, Dec 20 2021, 02:41:03) \n[GCC 9.4.0]' pysam.__version__='0.22.0' [3.9120245100930333, 3.912719252984971, 3.9148598960600793, 3.9105764548294246, 3.9074977058917284] sys.version='3.11.7 | packaged by conda-forge | (main, Dec 15 2023, 08:38:37) [GCC 12.3.0]' pysam.__version__='0.22.0' [3.736623673932627, 3.7335626899730414, 3.734525352017954, 3.734872733009979, 3.7376032220199704]
Is it normal? or did I miss something?
test code:
Results:
Is it normal? or did I miss something?