From 4fd4d41d81c0f34bf1eaa43769dd8dec8d04f353 Mon Sep 17 00:00:00 2001 From: Felix Van der Jeugt Date: Wed, 17 Feb 2021 10:22:14 +0100 Subject: [PATCH] use tab separator in import --- .github/workflows/static_database.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/static_database.yml b/.github/workflows/static_database.yml index 79e1d13..6bc7d14 100644 --- a/.github/workflows/static_database.yml +++ b/.github/workflows/static_database.yml @@ -35,11 +35,11 @@ jobs: sqlite3 output.db < workflows/static_database/structure.sql # Read all generated data into this database - zcat data/tables/ec_numbers.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin ec_numbers' - zcat data/tables/go_terms.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin go_terms' - zcat data/tables/interpro_entries.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin interpro_entries' - zcat data/tables/taxons.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin taxons' - zcat data/tables/lineages.tsv.gz | sed "s/\t/$/g" | sqlite3 -csv -separator "$" output.db '.import /dev/stdin lineages' + zcat data/tables/ec_numbers.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin ec_numbers' + zcat data/tables/go_terms.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin go_terms' + zcat data/tables/interpro_entries.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin interpro_entries' + zcat data/tables/taxons.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin taxons' + zcat data/tables/lineages.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin lineages' # Compress the database before uploading it to a Github release zip output.zip output.db