liftovergl.py --help usage: liftovergl.py [-h] [-g GLSTRING | -u URI | -j JSONFILE] [-s SOURCE] [-t TARGET] optional arguments: -h, --help show this help message and exit -g GLSTRING, --glstring GLSTRING GL String to be converted -u URI, --uri URI GL Service URI of GL String -f JSONFILE, --jsonfile JSONFILE input file containing JSON -s SOURCE, --source SOURCE Source IMGT/HLA version, e.g., '3.0.0' -t TARGET, --target TARGET Target IMGT/HLA version, e.g. '3.25.0'
Any of the following may be used for input:
- GLSTRING : GL String
- URI : URI pointing to a GL String,
- JSONFILE : JSON input file containing the URI and source and target namespaces
The JSONFILE input file uses the same JSON format used by the liftover service (https://gl.nmdp.org/liftover/)
Example JSONFILE input file:
{ sourceNamespace: https://gl.nmdp.org/imgt-hla/3.20.0/, sourceUri: https://gl.nmdp.org/imgt-hla/3.20.0/genotype/2i4, targetNamespace: https://gl.nmdp.org/imgt-hla/3.25.0/ }
Converts a GL String from one version of the IMGT/HLA database to another.
The program returns JSON formated output:
{ sourceGl: "input GL String to be converted" sourceUri: "URI of GL String registered in a GL service" targetGl: "GL String converted to a different IMGT/HLA version" targetUri: "URI of converted GL String" }
This program uses a AllelelistGgroups_history.txt
file which was created by
combining data from Allelelist_history.txt
, hml_ambigs.xml
, and
hla_nom_g.txt
files from https://github.com/ANHIG/IMGTHLA. The
AllelelistGgroups_history.txt
will need to regenerated every time a
new version of the IMGT/HLA database is released.
then mapped directly to alleles in the target version. If alleles do not exist in the target, then they are dropped from the target GL String. Alleles are not expanded to include new alleles. eg., the following alleles exist for 3.20.0 and 3.24.0:
HLA00053
HLA-A*24:03:01
HLA00053
HLA-A*24:03:01:01
HLA14804
HLA-A*24:03:01:02
HLA-A*24:03:01
is converted from 3.20.0 to 3.25.0, it gets assigned toHLA-A*24:03:01:01
and notHLA-A*24:03:01:01/HLA-A*24:03:01:02
This program has been tested using Python 3.6.
#!/usr/bin/env python3 import argparse import json import os import pandas import re import requests import sys
liftovergl.py
looks for AllelelistGgroups_history.txt
in the
directory that is pointed to by the IMGTHLA
environment variable.
If you use bash
, add something like this line in your
.bash_profile
or ~/.bashrc
file depending on where you would
like to store the file:
export IMGTHLA="$HOME/imgthla"
and copy the AllelelistGgroups_history.txt
file to $IMGTHLA
Using a GL String for input:
./liftovergl.py -g "HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:03:01" -s '3.20.0' -t '3.25.0' { "sourceGl": "HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:03:01", "sourceUri": "https://gl.nmdp.org/imgt-hla/3.20.0/genotype/2i4", "targetGl": "HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:03:01:01", "targetUri": "https://gl.nmdp.org/imgt-hla/3.25.0/genotype/p9" }
Using a URI for input:
./liftovergl.py -u "https://gl.nmdp.org/imgt-hla/3.20.0/genotype/2i4" -t '3.25.0' { "sourceGl": "HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:03:01", "sourceUri": "https://gl.nmdp.org/imgt-hla/3.20.0/genotype/2i4", "targetGl": "HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:03:01:01", "targetUri": "https://gl.nmdp.org/imgt-hla/3.25.0/genotype/p9" }
Using a JSON file with the example above for input:
./liftovergl.py -f genotype.json { "sourceGl": "HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:03:01", "sourceUri": "https://gl.nmdp.org/imgt-hla/3.20.0/genotype/2i4", "targetGl": "HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:03:01:01", "targetUri": "https://gl.nmdp.org/imgt-hla/3.25.0/genotype/p9" }
In the following example containing four alleles, three get dropped going from 3.18.0
to 3.25.0
,
and another's name is changed from HLA-A*26:03:02
to HLA-A*26:111
./liftovergl.py -g 'HLA-A*03:194+HLA-A*26:03:02^HLA-DRB1*11:11:02+HLA-DRB1*08:01:03' -s "3.18.0" -t "3.25.0" { "sourceGl": "HLA-A*03:194+HLA-A*26:03:02^HLA-DRB1*11:11:02+HLA-DRB1*08:01:03", "sourceUri": "https://gl.nmdp.org/imgt-hla/3.18.0/multilocus-unphased-genotype/k", "targetGl": "HLA-A*26:111", "targetUri": "https://gl.nmdp.org/imgt-hla/3.25.0/multilocus-unphased-genotype/uw" }
Same as above, but added HLA-B
locus:
./liftovergl.py -g 'HLA-A*03:194+HLA-A*26:03:02^HLA-B*40:10:01+HLA-B*44:03:01/HLA-B*44:03:02^HLA-DRB1*11:11:02+HLA-DRB1*08:01:03' -s "3.18.0" -t "3.25.0" { "sourceGl": "HLA-A*03:194+HLA-A*26:03:02^HLA-B*40:10:01+HLA-B*44:03:01/HLA-B*44:03:02^HLA-DRB1*11:11:02+HLA-DRB1*08:01:03", "sourceUri": "https://gl.nmdp.org/imgt-hla/3.18.0/multilocus-unphased-genotype/m", "targetGl": "HLA-A*26:111^HLA-B*40:10:01:01+HLA-B*44:03:01:01/HLA-B*44:03:02", "targetUri": "https://gl.nmdp.org/imgt-hla/4.25.0/multilocus-unphased-genotype/uy" }
multilocus-unphased-genotype containing a G-group:
./liftovergl.py -f mugG.json { "sourceGl": "HLA-A*01:01:01G+HLA-A*26:03:02^HLA-B*40:10:01+HLA-B*44:03:01/HLA-B*44:03:02", "sourceUri": "https://gl.nmdp.org/imgt-hla/3.18.0/multilocus-unphased-genotype/n", "targetGl": "HLA-A*01:01:01G+HLA-A*26:111^HLA-B*40:10:01:01+HLA-B*44:03:01:01/HLA-B*44:03:02", "targetUri": "https://gl.nmdp.org/imgt-hla/3.25.0/multilocus-unphased-genotype/uz" }