Add G groups, frequency data, and update protein sequence to

[apmody]

1. Add three and four field HLA alleles ("MHC gene allele") and corresponding nucleotide sequences.
2. Add terms for G groups
3. Choose "best" protein sequence for chain-sequences.tsv so that the longest protein sequence is chosen from all alleles that have the same first two-fields (e.g. choose the longest protein sequence between HLA-A*01:140:01 and HLA-A*01:140:02)
4. Add frequency data based on CIWD 3.0 data for different HLA alleles (data, paper)

[rvita]

For item #3, do you also update the accession and the resource name to match the new sequence?

…

On Tue, Mar 30, 2021 at 3:55 PM Apurva Mody ***@***.***> wrote: 1. Add three and four field HLA alleles ("MHC gene allele") and corresponding nucleotide sequences. 2. Add terms for G groups (http://hla.alleles.org/alleles/g_groups.html ) 3. Choose "best" protein sequence forchain-sequences.tsv so that the longest protein sequence is chosen from all alleles that have the same first two-fields (e.g. choose the longest protein sequence between HLA-A*01:140:01 and HLA-A*01:140:02) 4. Add frequency data based on CIWD 3.0 data for different HLA alleles (data <https://www.ihiw18.org/component-immunogenetics/download-common-and-well-documented-alleles-3-0/>, paper <https://onlinelibrary.wiley.com/doi/full/10.1111/tan.13811> ------------------------------ You can view, comment on, or merge this pull request online at: #90 Commit Summary - First pass: Get G groups, get full CDS sequences, import population group terms - Reworked parsing of hla.dat file, add template strings - Get appropriate exons for G group when MHC allele is class I (exon 2 and 3) or class II (exon 2) - Merge branch 'master' into G_group - Added code to add terms to index.tsv and error report - Merge branch 'master' into G_group - Changed template strings - Added alleles which have partial sequence - Organized gen_allele_update_seq.py into functions, Modified import.txt - First pass at extracting population frequency data - Merge branch 'master' into G_group - Added code to verify accession numbers from frequency data and build/hla.dat file - Second pass adding population frequency data for chains, G groups, reworked index update code - Add frequency of gene_alleles - Added helper function for getting G group exons, removed requirement for protein match between current MRO and allele - Fix protein sequence to get best protein sequence File Changes - *M* Makefile <https://github.com/IEDB/MRO/pull/90/files#diff-76ed074a9305c04054cdebb9e9aad2d818052b07091de1f20cad0bbac34ffb52> (38) - *M* index.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-03713472c9d385b498690e3c0f507cd67f378e9db1f2ef63711897c392c2ed7e> (27251) - *A* ontology/G-group-frequencies.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-701bac6402654020951e3c390d75587dd4756261438e663cdda7832394e7690e> (277) - *A* ontology/G-group.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-176f1865135d177fb0e7f02ac311066b2b935963d6d3d259b98f40f55e7cf750> (514) - *A* ontology/chain-frequencies.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-9ed7c8aa1d1ccac9b602d7c96c8643687e2485db3738cf4268127567d03f02dc> (784) - *M* ontology/chain-sequence.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-93686f7a9062e877738eb4ef9e8bac75995fd7c448012a9f57dfcddbf79b29c7> (727) - *M* ontology/core.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-cce693e5e496c2640c02d0f726ef8c1b40657ba6389aee1b1040d246ad55494d> (2) - *A* ontology/frequency-properties.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-3ccc40ddae15df9428e8a3ad74ccddb26dd834f2e18b3585011dbedbdf2b527c> (10) - *A* ontology/gene-allele-frequencies.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-150e1823d5eff9a49e96fe52034affca6e0ae7019c325cd9d35e99ed5804d9a0> (8427) - *A* ontology/gene-alleles.tsv <https://github.com/IEDB/MRO/pull/90/files#diff-91369a4d23b970756c572cca4d3e92f1e572e04fc5a373f82cd5ef9b5314e732> (26731) - *M* ontology/import.txt <https://github.com/IEDB/MRO/pull/90/files#diff-5a8021ed1bc10adb45b4669b0a9b18150676f1e4c5d637eda5219bb499a66dc4> (9) - *M* requirements.txt <https://github.com/IEDB/MRO/pull/90/files#diff-4d7c51b1efe9043e44439a949dfd92e5827321b34082903477fd04876edb7552> (1) - *M* src/scripts/prefixes.sql <https://github.com/IEDB/MRO/pull/90/files#diff-fab310065ad989bdb99a832e186f9952e28139b74e172b566ca8944b2f5746f0> (5) - *A* src/update_gene_allele_seq.py <https://github.com/IEDB/MRO/pull/90/files#diff-494ef043e3467db44f01ea1e46731661c064f5f6e52369884cb31b7012957d8d> (499) Patch Links: - https://github.com/IEDB/MRO/pull/90.patch - https://github.com/IEDB/MRO/pull/90.diff — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#90>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADKDY422AMITODDDRD2A6YTTGJJFFANCNFSM42DEXWVQ> .

-- Randi Vita, M.D. Lead Ontology and Quality Manager Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology 9420 Athena Circle La Jolla, Ca 92037 ***@***.*** www.immuneepitope.org 858-752-6912

[apmody]

For item #3, do you also update the accession and the resource name to match the new sequence?

Yes, I have added the accession and the resource name as it appears in IMGT.

[jamesaoverton]

This make mro.owl task must pass before this can be merged. It's failing for me locally and here in GitHub Actions.