From ef43c79201bfa01217266de4da0d283562f48423 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alfonso=20Mu=C3=B1oz-Pomer=20Fuentes?= Date: Thu, 12 Oct 2023 15:35:48 +0100 Subject: [PATCH] Add section to README to load/delete experiment design in Postgres --- README.md | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 55e0f61..e8755b5 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Single Cell Expression Atlas database loading module (v1.0.0) +# Single Cell Expression Atlas database loading module (v2.0.0) A [Single Cell Expression Atlas](https://www.ebi.ac.uk/gxa/sc) module for loading experiments to a Postgres 11 database. Release v0.4.0 was used for [the October 2022 data release of Single Cell Expression @@ -63,7 +63,7 @@ export dbConnection=... delete_db_scxa_dimred.sh ``` -## `scxa_cell_group` and `scxa_cell_group_membership` table +## `scxa_cell_group` and `scxa_cell_group_membership` tables ### Load data Run `bin/load_db_scxa_cell_clusters.sh`. It requires the following environment variables: @@ -117,6 +117,25 @@ export dbConnection=... delete_db_scxa_marker_genes.sh ``` +## `exp_design` and `exp_design_column` tables + +### Load data +Run `bin/load_exp_design.sh`. It requires the following environment variables: + +| Variable name | Description | +|-----------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| `CONDENSED_SDRF_FILE` | Path of the condensed SDRF file of the experiment being loaded | +| `SDRF_FILE` | Path of the SDRF file of the experiment being loaded | +| `dbConnection` | A Postgres connection string in the form `postgresql://{user}:{password}@{host:port}/{databaseName}` pointing to a Postgres 11 server where the expected `scxa_cell_group_marker_genes` and `scxa_cell_group_marker_gene_stats` tables exist | + +### Delete data +Currently, there’s no script to delete data from these tables. You can do it manually with the following SQL statements: + +```sql +DELETE FROM exp_design WHERE exp_design_column_id IN (SELECT id FROM exp_design_column WHERE experiment_accession='E-FOO-123'); +DELETE FROM exp_design_column WHERE experiment_accession='E-FOO-123'; +``` + ## Post-loading a batch of experiments Once a number of experiments have been loaded, tables should be re-indexed: