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5. Query

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.

5.1 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 distances 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.

5.2 Output files format

{output_prefix}_features_count_per_group.tsv

A TSV file containing two columns, the first column is the supergroup name and the second column is the number of features that are contained in that supergroup, and the third column is a PIPE-separated list of supergroups from the user query that are associated with the feature in the first column.

{output_prefix}_features_count_per_group_histogram.png

A histogram plot showing the distribution of the number of features per supergroup.