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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
151 stars 46 forks source link

[obophenotype/human-phenotype-ontology] Release v2022-01-27 - 2023-01-27 Release #3781

Closed dnil closed 1 year ago

dnil commented 1 year ago

2023-01-27 Release

Repository: obophenotype/human-phenotype-ontology · Tag: v2022-01-27 · Commit: 5957997 · Released by: matentzn

What's Changed

Make sure the hp.json version is copied correctly into HPOA by @matentzn in #9566 Return of the diff by @matentzn in #9600 Prepare HPO release by @matentzn in #9602 Full Changelog: v2022-12-15...v2022-01-27

northwestwitch commented 1 year ago

Perfect timing, perhaps we manage updating already next week!

dnil commented 1 year ago

Testing on stage:

scout download everything --api-key nNNNs
scout update genes --build 37 -f .
scout update genes --build 38 -f .
scout update omim --api-key nNNNs --institute cust002 --genemap2 genemap2.txt --mim2genes mim2genes.txt
scout update diseases -f .
scout update hpo --hpoterms hpo.obo --hpo-to-genes phenotype_to_genes.txt
...
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.omim[6968] INFO Number of genes without hgnc symbol 122
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.omim[6968] INFO Parsing the omim genemap2
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol TRU-TCA1-1 does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol DISC2 does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol ATXN8 does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol NOTCH2NLC does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol NUTM2B-AS1 does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol PERCC1 does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol HRURF does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol CIROP does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol MYMX does not exist
2023-02-03 14:16:45 hasta.scilifelab.se scout.parse.panel[6968] WARNING Gene symbol CFAP74 does not exist
2023-02-03 14:16:46 hasta.scilifelab.se scout.build.panel[6968] INFO Building panel with name: OMIM-AUTO
2023-02-03 14:16:47 hasta.scilifelab.se scout.build.panel[6968] WARNING Symbol in database does not correspond to symbol in panel file for gene 21219
2023-02-03 14:16:47 hasta.scilifelab.se scout.build.panel[6968] WARNING Using symbol CILK1 for gene 21219, instead of MAP3K20
2023-02-03 14:16:48 hasta.scilifelab.se scout.adapter.mongo.panel[6968] INFO Updating versions for new genes
2023-02-03 14:16:48 hasta.scilifelab.se scout.adapter.mongo.panel[6968] INFO Updated 4442 genes
2023-02-03 14:16:48 hasta.scilifelab.se scout.adapter.mongo.panel[6968] INFO loading panel OMIM-AUTO, version 20.0 to database
2023-02-03 14:16:48 hasta.scilifelab.se scout.adapter.mongo.panel[6968] INFO Nr genes in panel: 4443
2023-02-03 14:16:48 hasta.scilifelab.se scout.adapter.mongo.panel[6968] INFO Fetch gene panel OMIM-AUTO, version 20.0 from database
2023-02-03 14:16:48 hasta.scilifelab.se scout.adapter.mongo.panel[6968] DEBUG Panel saved
...
2023-02-03 14:18:47 hasta.scilifelab.se scout.adapter.mongo.omim[14476] DEBUG Disease term saved
2023-02-03 14:18:47 hasta.scilifelab.se scout.load.hpo[14476] INFO Loading done. Nr of diseases loaded 7433
2023-02-03 14:18:47 hasta.scilifelab.se scout.load.hpo[14476] INFO Time to load diseases: 0:00:05.479525
2023-02-03 14:18:47 hasta.scilifelab.se scout.commands.update.disease[14476] INFO Successfully loaded all disease terms
...
2023-02-03 14:23:22 hasta.scilifelab.se scout.build.hpo[28908] DEBUG Building hpo term HP:5000048
Loading hpo terms  [####################################]  100%          2023-02-03 14:23:22 hasta.scilifelab.se scout.adapter.mongo.hpo[28908] DEBUG Loading hpo bulk
...
2023-02-03 14:23:23 hasta.scilifelab.se scout.load.hpo[28908] INFO Loading done. Nr of terms loaded 17245
2023-02-03 14:23:23 hasta.scilifelab.se scout.load.hpo[28908] INFO Time to load terms: 0:00:02.631290
dnil commented 1 year ago

🏁 🏁 ✅ And same on prod!