running time about stringmlst HOT 1 CLOSED

Hi Alessandro,

Happy new year, too!

This boils down to a difference in what we're reporting. stringMLST is reporting the processing time per sample (i.e. the amount of time spent inside the singleSampleTool or singleFileTool functions) and not the total runtime of the program. This was done so that we could track per-sample runtimes for multi-sample runs.

If we put timing statements around the main() code it matches the time stringMLST.py ... reported value

stringMLST-issue45.txt

https://github.com/jordanlab/stringMLST/blob/issue45/stringMLST.py#L1592-L1617

time ./issue45/stringMLST.py --predict -1 tests/fastqs/ERR026529_1.fastq -2 tests/fastqs/ERR026529_2.fastq -P neisseria/nmb -t
Sample  abcZ    adk     aroE    fumC    gdh     pdhC    pgm     ST      Time
ERR026529       231     180     306     612     269     277     260     10174   4.20
Total runtime:  7.498115539550781
./issue45/stringMLST.py  --predict -1 tests/fastqs/ERR026529_1.fastq   7.48s user 1.05s system 99% cpu 8.535 total

from stringmlst.