hlarp

Normalize HLA typing output of Seq2HLA, Optitype & ATHLATES.

Hlarp is also provided as a library.

Pronounced "heh-larp" (or with a soft 'h' : "larp").

Installation

The easiest way to install the tool is to "opam pin" this repository:

opam pin add -k git https://github.com/hammerlab/hlarp

Now you can run hlarp with hlarp.

Using hlarp

Command line

Aggregating results

hlarp seq2HLA /path/to/seq2HLA/results directory > results.csv
hlarp optitype /path/to/OptiType/results directory > results.csv

The output is a csv

class	allele	confidence	run
1	A*02:05:01	0.500000	120013
1	A*30:01:01	0.500000	120013
1	B*57:03:01	1.000000	120013
1	B*57:03:01	1.000000	120013
1	C*18:02	1.000000	120013
1	C*18:02	1.000000	120013
2	DRB1*03:02:01	0.500000	120013
2	DRB1*15:03:01:01	0.250000	120013
2	DRB3*01:01:02:01	0.500000	120013
2	DRB3*01:01:02:02	0.500000	120013
2	DRB5*01:01:01	1.000000	120013
2	DRB5*01:01:01	1.000000	120013
1	A*31:01:02	0.500000	120021
1	A*31:01:13	0.500000	120021
1	C*02:10	1.000000	120021
1	C*02:10	1.000000	120021
2	DRB1*15:03:01:01	0.500000	120021
2	DRB1*15:03:01:02	0.500000	120021
2	DRB3*02:02:01:01	0.500000	120021
2	DRB3*02:02:01:02	0.500000	120021
2	DRB5*01:01:01	1.000000	120021
2	DRB5*01:01:01	1.000000	120021
1	A*68:02:01:01	0.166667	120074
1	A*74:01	0.500000	120074
1	B*15:03:01	0.500000	120074
1	B*15:16:01	0.500000	120074
1	C*02:10	0.500000	120074
1	C*16:01:01	0.500000	120074
2	DRB1*01:02:01	0.500000	120074
2	DRB1*14:54:01	0.500000	120074

Some columns are left empty due to the nature of the HLA-typer.

Comparison

hlarp compare --resolution 2 -l A -l B -l C --loci DRB1 --optitype /path/to/optitype/results -a /path/to/ATHLATES/results/

Will generate this kind of report:

120013  jacard similarities: 1.00 1.00 0.00 0.00
    A:  A*02:05 OptiType;ATHLATES
        A*30:01 OptiType;ATHLATES
    B:  B*57:03 OptiTypex2;ATHLATESx2
    C:  C*18:01 OptiTypex2
        C*18:02 ATHLATESx2
    DRB1:   DRB1*03:02  ATHLATES
        DRB1*15:03  ATHLATES
120021  jacard similarities: 0.33 0.00 0.33 0.00
    A:  A*02:01 OptiType
        A*31:01 OptiType;ATHLATESx2
    B:  B*15:03 OptiType
        B*45:01 OptiType
    C:  C*02:10 OptiType;ATHLATESx2
        C*16:01 OptiType
    DRB1:   DRB1*15:03  ATHLATESx2
120074  jacard similarities: 1.00 1.00 1.00 0.00
    A:  A*68:02 OptiType;ATHLATES
        A*74:01 OptiType;ATHLATES
    B:  B*15:03 OptiType;ATHLATES
        B*15:16 OptiType;ATHLATES
    C:  C*02:10 OptiType;ATHLATES
        C*16:01 OptiType;ATHLATES
    DRB1:   DRB1*01:02  ATHLATES
        DRB1*14:54  ATHLATES
...
Average jacard similarities across runs: 0.54 0.60 0.51 0.07

From OCaml top

You can also use the hlarp module:

open Hlarp

hammerlab / hlarp

readme