grr_browse

grr_browse lists the resources of the GRRs that a GRR definition file names. It reads the GRR definition from -g, from the GRR_DEFINITION_FILE environment variable or from ~/.grr_definition.yaml, in that order, and uses the default IossifovLab GRR when it finds none. It prints the definition that it uses, then one line for each resource: the type, the version, the file count, the size, the GRR and the resource id. It writes no files. Use it to check which GRRs GAIn sees and to find a resource id for an annotation pipeline.

Examples

grr_browse -g my_grr_definition.yaml

Lists every resource of the GRRs in my_grr_definition.yaml.

grr_browse -t position_score -s phyloP

Lists the position scores that match the full-text search term phyloP.

grr_browse -q 'hg38/scores/*' --summary

Lists the resources whose ids match the wildcard query, each with its summary.

See also

Option reference

Genomic Resource Repository Browse Tool

usage: grr_browse [-h] [--version] [--verbose] [--logfile LOGFILE] [-g GRR]
                  [-s SEARCH] [-t TYPE] [-q QUERY] [--summary] [--bytes]

Named Arguments

--version

Prints the GAIn version and exits.

Default: False

--verbose, -v, -V

Default: 0

--logfile

File to log output to. If not set, logs to console.

--bytes

Print the resource size in bytes

Default: False

Repository/Resource

-g, --grr

path to GRR definition file.

-s, --search

FTS search term to filter resources. A term may name one index column, e.g. ‘assay_term_name: “ATAC-seq”’, but the columns are per-repository – across a group, a repository that does not index the column is skipped with a warning rather than searched. Use -q to select on labels independently of any index.

-t, --type

Filter resources by type.

-q, --query

Filter resources by a wildcard query over the resource id and labels, e.g. ‘hg38/scores/[phenotype=”autism”]’. A label a resource does not carry reads as empty, so [key=””] holds for every resource rather than selecting the ones that have the label.

--summary

Print a summary for each resource below its listing line.

Default: False