hammerlab/hlarp

Name: hlarp

Owner: Hammer Lab

Description: Normalize HLA typing output.

Created: 2016-04-16 06:14:36.0

Updated: 2016-11-07 04:25:28.0

Pushed: 2017-04-07 01:31:29.0

Homepage: null

Size: 81

Language: OCaml

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README

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:

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

Now you can run hlarp with hlarp.

Using hlarp

Command line

Aggregating results

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

The output is a csv

| class | allele | qualifier | confidence | run | |——-|——————|———–|————|——–| | 1 | A02:05:01 | | 0.500000 | 120013 | | 1 | A30:01:01 | | 0.500000 | 120013 | | 1 | B57:03:01 | | 1.000000 | 120013 | | 1 | B57:03:01 | | 1.000000 | 120013 | | 1 | C18:02 | | 1.000000 | 120013 | | 1 | C18:02 | | 1.000000 | 120013 | | 2 | DRB103:02:01 | | 0.500000 | 120013 | | 2 | DRB115:03:01:01 | | 0.250000 | 120013 | | 2 | DRB301:01:02:01 | | 0.500000 | 120013 | | 2 | DRB301:01:02:02 | | 0.500000 | 120013 | | 2 | DRB501:01:01 | | 1.000000 | 120013 | | 2 | DRB501:01:01 | | 1.000000 | 120013 | | 1 | A31:01:02 | | 0.500000 | 120021 | | 1 | A31:01:13 | | 0.500000 | 120021 | | 1 | C02:10 | | 1.000000 | 120021 | | 1 | C02:10 | | 1.000000 | 120021 | | 2 | DRB115:03:01:01 | | 0.500000 | 120021 | | 2 | DRB115:03:01:02 | | 0.500000 | 120021 | | 2 | DRB302:02:01:01 | | 0.500000 | 120021 | | 2 | DRB302:02:01:02 | | 0.500000 | 120021 | | 2 | DRB501:01:01 | | 1.000000 | 120021 | | 2 | DRB501:01:01 | | 1.000000 | 120021 | | 1 | A68:02:01:01 | | 0.166667 | 120074 | | 1 | A74:01 | | 0.500000 | 120074 | | 1 | B15:03:01 | | 0.500000 | 120074 | | 1 | B15:16:01 | | 0.500000 | 120074 | | 1 | C02:10 | | 0.500000 | 120074 | | 1 | C16:01:01 | | 0.500000 | 120074 | | 2 | DRB101:02:01 | | 0.500000 | 120074 | | 2 | DRB114:54:01 | | 0.500000 | 120074 |

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

Comparison

p 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:

13  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
21  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
74  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

age jacard similarities across runs: 0.54 0.60 0.51 0.07

From OCaml top

You can also use the hlarp module:

 Hlarp