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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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