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IMGT update #34

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acrinklaw wants to merge 9 commits into from
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IMGT update #34

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12be1db
Update ontology tables with missing IMGT alleles, add script to automate
Aug 15, 2020
0204bd8
Add check_missing_alleles.py
Aug 15, 2020
53f9f00
Format with black, clean up comments
Aug 15, 2020
bf7cd32
Fix duplicate bug in index.tsv
Aug 16, 2020
fc06c4a
Add molecule.tsv update, clean up script
Aug 26, 2020
1f2731c
Add formatting to check_missing_alleles
Aug 26, 2020
5c000ba
Sort output files, fix formatting of molecule.tsv
Aug 26, 2020
b1dde6f
Update index to current and add new terms, rebuild mro.owl
Aug 27, 2020
26b88c2
Change write to csv writer, add task to makefile, change hardcoded pa…
Aug 27, 2020
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9 changes: 9 additions & 0 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,15 @@ build/dla.fasta: | build
update-seqs: src/update_seqs.py ontology/chain-sequence.tsv build/hla.fasta build/sla.fasta build/dla.fasta
python3 $^

build/hla_prot.fasta: | build
curl -o $@ -L https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/hla_prot.fasta

build/AlleleList.txt: | build
curl -o $@ -L https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/Allelelist.txt

.PHONY: update-alleles
update-alleles: src/check_missing_alleles.py ontology/chain-sequence.tsv ontology/chain.tsv ontology/molecule.tsv ontology/genetic-locus.tsv index.tsv build/hla_prot.fasta build/AlleleList.txt
python3 $^

### OWL Files

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34,626 changes: 34,550 additions & 76 deletions index.tsv
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821,285 changes: 821,033 additions & 252 deletions mro.owl
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15,393 changes: 15,355 additions & 38 deletions ontology/chain-sequence.tsv
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15,824 changes: 15,785 additions & 39 deletions ontology/chain.tsv
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29 changes: 29 additions & 0 deletions ontology/genetic-locus.tsv
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Expand Up @@ -45,20 +45,49 @@ HLA-B locus subclass human MHC class I locus
HLA-BTN3A locus subclass human non-classical MHC locus
HLA-C locus subclass human MHC class I locus
HLA-CD1 locus subclass human non-classical MHC locus
HLA-DMA locus subclass human MHC class II locus
HLA-DMB locus subclass human MHC class II locus
HLA-DOA locus subclass human MHC class II locus
HLA-DOB locus subclass human MHC class II locus
HLA-DPA1 locus subclass human MHC class II locus
HLA-DPA2 locus subclass human MHC class II locus
HLA-DPA locus subclass human MHC class II locus
HLA-DPB1 locus subclass human MHC class II locus
HLA-DPB2 locus subclass human MHC class II locus
HLA-DPB locus subclass human MHC class II locus
HLA-DQA locus subclass human MHC class II locus
HLA-DQB locus subclass human MHC class II locus
HLA-DRA locus subclass human MHC class II locus
HLA-DRB1 locus subclass HLA-DRB locus
HLA-DRB2 locus subclass human MHC class II locus
HLA-DRB3 locus subclass HLA-DRB locus
HLA-DRB4 locus subclass HLA-DRB locus
HLA-DRB5 locus subclass HLA-DRB locus
HLA-DRB6 locus subclass human MHC class II locus
HLA-DRB7 locus subclass human MHC class II locus
HLA-DRB8 locus subclass human MHC class II locus
HLA-DRB9 locus subclass human MHC class II locus
HLA-DRB locus subclass human MHC class II locus
HLA-E locus subclass human non-classical MHC locus
HLA-F locus subclass human non-classical MHC locus
HLA-G locus subclass human non-classical MHC locus
HLA-H locus subclass human non-classical MHC locus
HLA-HFE locus subclass human non-classical MHC locus
HLA-J locus subclass human non-classical MHC locus
HLA-K locus subclass human non-classical MHC locus
HLA-L locus subclass human non-classical MHC locus
HLA-MICA locus subclass human MHC class I locus
HLA-MICB locus subclass human MHC class I locus
HLA-MR1 locus subclass human non-classical MHC locus
HLA-P locus subclass human non-classical MHC locus
HLA-S locus subclass human non-classical MHC locus
HLA-T locus subclass human non-classical MHC locus
HLA-TAP1 locus subclass human MHC class I locus
HLA-TAP2 locus subclass human MHC class I locus
HLA-U locus subclass human non-classical MHC locus
HLA-V locus subclass human non-classical MHC locus
HLA-W locus subclass human non-classical MHC locus
HLA-Y locus subclass human non-classical MHC locus
MHC class I locus subclass MHC locus
MHC class II locus subclass MHC locus
Mafa-DQA locus subclass crab-eating macaque MHC class II locus
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18,773 changes: 18,736 additions & 37 deletions ontology/molecule.tsv
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