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hammerlab / hlarp

Normalize HLA typing output.
Apache License 2.0
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Add comparison features #14

Closed rleonid closed 8 years ago

rleonid commented 8 years ago

The results look like

$ ./hlarp_cli.native compare --resolution 2 -c 1 -c 2 --optitype /path/to/opti_results/ -a /path/to/athlates_results/
...
207956_ACAGTG   jacard similarities: 0.2500000.000000
    1:  A*23:01 OptiType
        A*34:02 OptiType
        B*13:02 OptiType;ATHLATES
        B*81:01 OptiType
        B*81:03 ATHLATES
        C*08:04 OptiType;ATHLATES
        C*18:01 OptiType
        C*18:02 ATHLATES
    2:  DRB1*12:01  ATHLATES
        DRB1*15:03  ATHLATES
        DRB3*01:01  ATHLATESx2
        DRB5*01:01  ATHLATESx2
207978_CTTGTA   jacard similarities: 0.7142860.000000
    1:  A*29:02 OptiType;ATHLATES
        A*32:01 OptiType;ATHLATES
        B*15:16 OptiType;ATHLATESx2
        B*81:01 OptiType
        C*16:01 OptiType;ATHLATES
        C*18:01 OptiType;ATHLATES
    2:  DRB1*01:02  ATHLATES
        DRB1*11:01  ATHLATES
        DRB3*03:01  ATHLATESx2
Average jacard similarities across runs: 0.5147350.050000
ihodes commented 8 years ago

LGTM, just thinking it might be nicer in lieu of 1 and 2 in the results to have I and II for MHC class I and II. NBD either way.

rleonid commented 8 years ago

That was going to be the original format, but the csv output uses '1' and '2', so I wanted to be consistent.