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Update scripts #121

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0bbaa6c
Add new update script
acrinklaw Sep 27, 2021
562d974
Change update script to accept HLA alleles
acrinklaw Sep 27, 2021
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4 changes: 2 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -208,8 +208,8 @@ build/hla_prot.fasta: | build
build/AlleleList.txt: | build
curl -o $@ -L https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/Allelelist.txt

.PHONY: update-mhcflurry-alleles
update-mhcflurry-alleles: src/scripts/alleles/update_alleles_mhcflurry.py ontology/chain-sequence.tsv ontology/chain.tsv ontology/molecule.tsv ontology/genetic-locus.tsv index.tsv build/mhc.fasta iedb/iedb.tsv
.PHONY: update-alleles
update-alleles: src/scripts/alleles/update_alleles.py ontology/chain-sequence.tsv ontology/chain.tsv ontology/molecule.tsv ontology/genetic-locus.tsv index.tsv build/mhc.fasta iedb/iedb.tsv src/scripts/alleles/locus_data.json build/hla.fasta
python3 $^

### OWL Files
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22 changes: 22 additions & 0 deletions src/scripts/alleles/locus_data.json
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@@ -1,5 +1,27 @@
{
"species": [
{
"mhc_code": "HLA",
"taxon": "human",
"class_I": [
"A",
"B",
"C"
],
"pairing": {
"DQA": "DQB",
"DRA": "DRB",
"DPA": "DPB"
},
"pairing_rev": {
"DQB": "DQA",
"DRB1": "DRA",
"DRB3": "DRA",
"DRB4": "DRA",
"DRB5": "DRA",
"DPA": "DPB"
}
},
{
"mhc_code": "Onmy",
"taxon": "rainbow trout",
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