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Add G domain (peptide biding region) sequence to HLA chain terms. #109

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Add G domain (peptide biding region) sequence to HLA chain terms. #109

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fe83cb8
First pass extracting G_domain
apmody Jul 20, 2021
920f9bf
Correction of splicing in exon 1. Write to ontology template.
apmody Jul 20, 2021
da9faa9
Add ontology templates.
apmody Jul 22, 2021
c4bab34
Update Makefile with new templates and rules.
apmody Jul 22, 2021
bb3a53e
Add ROBOT template string and term to index.tsv
apmody Jul 22, 2021
41b2f5c
Add Biopython to requirements.txt
apmody Jul 22, 2021
bb5851c
Fixed Makefile spelling mistake and minimal HLA G domain
apmody Jul 30, 2021
0ea37fb
Added Excluded Genes and logging messages
apmody Jul 30, 2021
bdce291
Refined logging of Biopython warnings
apmody Aug 4, 2021
e5fb23d
Merge branch 'master' into G_domain
apmody Aug 4, 2021
c579246
Parse log file
apmody Aug 4, 2021
e347cd5
Update index.tsv and properties.tsv with term G domain term
apmody Aug 4, 2021
e97e83b
Add G domain to chain-sequence.tsv, first pass
apmody Aug 4, 2021
22e5acc
Add G domain to chain-sequence.tsv, second pass
apmody Aug 5, 2021
a1c80c5
Add G domain sequence to chain-sequence.tsv
apmody Aug 5, 2021
7e083e1
Removed exclusion of null alleles
apmody Aug 5, 2021
d17f958
Remove G-domain-sequence.tsv
apmody Aug 5, 2021
a40500f
Removed properties.tsv
apmody Aug 5, 2021
d9771a4
Changed logging level, moved import csv to top of file.
apmody Aug 5, 2021
ce5a9c1
Removed properties.tsv from Makefile
apmody Aug 5, 2021
4410ae2
Double import for csv file
apmody Aug 5, 2021
0cfc6fe
Script changes and trailing tab endings fix
apmody Aug 11, 2021
6839760
Merge branch 'master' into G_domain
apmody Oct 7, 2021
616f956
Reupdated G domain in ontology/chain-sequence
apmody Oct 7, 2021
40bccc5
Added comments to G domain script.
apmody Oct 7, 2021
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7 changes: 7 additions & 0 deletions Makefile
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Expand Up @@ -187,6 +187,9 @@ build/hla.fasta: | build
build/mhc.fasta: | build
curl -L -o $@ ftp://ftp.ebi.ac.uk/pub/databases/ipd/mhc/MHC_prot.fasta

build/hla.dat: | build
curl -o $@ -L https://github.com/ANHIG/IMGTHLA/raw/Latest/hla.dat

# update-seqs will only write seqs to terms without seqs
.PHONY: update-seqs
update-seqs: src/scripts/update_seqs.py ontology/chain-sequence.tsv build/hla.fasta build/mhc.fasta
Expand All @@ -212,6 +215,10 @@ build/AlleleList.txt: | build
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
python3 $^

.PHONY: update-G-domain
update-G-domain: build/hla.dat
python3 src/scripts/alleles/G_domain.py

### OWL Files

mro.owl: build/mro-import.owl index.tsv $(build_files) ontology/metadata.ttl | build/robot.jar
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1 change: 1 addition & 0 deletions index.tsv
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Expand Up @@ -51201,3 +51201,4 @@ MRO:0051199 Atbe-B*01 protein complex owl:Class
MRO:0051200 BoLA-3*084:01N protein complex owl:Class
MRO:0051201 BoLA-3*086:01N protein complex owl:Class
MRO:0051202 BoLA-3*098:01N protein complex owl:Class
MRO:0051203 minimal HLA G domain sequence owl:AnnotationProperty
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