From c8b2c3a390d56bcc07406926ba45080a4b4dd74c Mon Sep 17 00:00:00 2001 From: project-defiant Date: Fri, 6 Dec 2024 14:47:56 +0100 Subject: [PATCH] feat: update default command help --- .../commands/update_gwas_curation_metadata.py | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/src/gentroutils/commands/update_gwas_curation_metadata.py b/src/gentroutils/commands/update_gwas_curation_metadata.py index 8bb42bd..023b48e 100644 --- a/src/gentroutils/commands/update_gwas_curation_metadata.py +++ b/src/gentroutils/commands/update_gwas_curation_metadata.py @@ -63,9 +63,7 @@ async def update_gwas_curation_metadata_command( This is the script to fetch the latest GWAS Catalog data files that include: - [x] gwas-catalog-associations_ontology-annotated.tsv - list of associations with ontology annotations by GWAS Catalog - [x] gwas-catalog-download-studies-v1.0.3.1.txt - list of published studies by GWAS Catalog - - [x] gwas-catalog-unpublished-studies-v1.0.3.1.tsv - list of unpublished studies by GWAS Catalog - [x] gwas-catalog-download-ancestries-v1.0.3.1.txt - list of published studies by GWAS Catalog - - [x] gwas-catalog-unpublished-ancestries-v1.0.3.1.tsv - list of unpublished studies by GWAS Catalog \b By default all GWAS Catalog data files are uploaded from GWAS Catalog FTP server to Open Targets GCP bucket. @@ -74,13 +72,9 @@ async def update_gwas_curation_metadata_command( \b gentroutils --log-file gs://gwas_catalog_data/curated_inputs/log.txt update-gwas-curation-metadata \\ - -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations_ontology-annotated.tsv gs://gwas_catalog_data/curated_inputs/gwas_catalog_associations_ontology_annotated.tsv \\ - -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-studies-v1.0.3.1.txt gs://gwas_catalog_data/curated_inputs/gwas_catalog_download_studies.tsv \\ - -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-unpublished-studies-v1.0.3.1.tsv gs://gwas_catalog_data/curated_inputs/gwas_catalog_unpublished_studies.tsv \\ - -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-ancestries-v1.0.3.1.txt gs://gwas_catalog_data/curated_inputs/gwas_catalog_download_ancestries.tsv \\ - -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-unpublished-ancestries-v1.0.3.1.tsv gs://gwas_catalog_data/curated_inputs/gwas_catalog_unpublished_ancestries.tsv \\ - -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/harmonised_list.txt gs://gwas_catalog_data/curated_inputs/harmonised_list.txt \\ - -f https://raw.githubusercontent.com/opentargets/curation/master/genetics/GWAS_Catalog_study_curation.tsv gs://gwas_catalog_data/manifests/gwas_catalog_study_curation.tsv \\ + -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations_ontology-annotated.tsv gs://gwas_catalog_data/gwas_catalog_associations_ontology_annotated.tsv \\ + -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-studies-v1.0.3.1.txt gs://gwas_catalog_inputs/gwas_catalog_download_studies.tsv \\ + -f ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-download-ancestries-v1.0.3.1.txt gs://gwas_catalog_inputs/gwas_catalog_download_ancestries.tsv \\ -g https://www.ebi.ac.uk/gwas/api/search/stats