Querying a DBRetina index
Query a DBRetina index with a set of groups (provided as a single-column file or cluster IDs in a DBRetina cluster file).
Usage: DBRetina query [OPTIONS]
Query DBRetina index.
Detailed description:
Query a DBRetina index with a set of groups (provided as a single-column
file or cluster IDs in a DBRetina cluster file). Output each feature and
the associated supergroups.
Examples:
1- groups file | DBRetina query -i index_prefix -g
groups_file -o output_prefix
2- clusters file with cluster IDs | DBRetina query -i index_prefix
--clusters-file clusters_file --cluster-ids 1,2,3 -o output_prefix
Options:
-i, --index-prefix TEXT index file prefix [required]
-g, --groups-file PATH single-column supergroups file
--clusters-file PATH DBRetina clusters file
--cluster-ids TEXT comma-separated list of cluster IDs
-o, --output TEXT output file prefix [required]
--help Show this message and exit.
Command arguments
-i, --index-prefix TEXT Index file prefix [required]
This is the user-defined prefix that was used in the indexing step.
-g, --groups-file PATH single-column supergroups file
This will filter out all pairwise similarities that are between supergroups that are not in the provided groups file. The groups file is a single-column file that contains the names of the supergroups to be included in the filtering.
--cluster-ids TEXT comma-separated list of cluster IDs
The cluster IDs selected from the clusters file. This argument is only used if the clusters file is not provided.
-o, --output TEXT output file prefix [required]
The output prefix that should be unique for this query.
Output files format
{output_prefix}_feature_to_groups.tsv
A three-columns TSV file containing the feature name, the number of supergroups associated with that feature, and a PIPE-separated list of supergroups associated with that feature.
Created: July 5, 2023