pgxdb_generate_collections.pl Perl Code Documentation

The pgxdb_generate_collections.pl script performs aggregation functions on databases, specifically the generation of collections for pre-calculated CNV frequencies and other statistics for samples grouped by different biocharachteristics.type.id or external_references.type.id values.

The script uses the PGXDB package and its configuration file.

Arguments

Output

The script will generate the aggregation collections in the -path directory. At the end of processing each collection, and at the end of the script, the commands to update the corresponding MongoDB collection will be shown in the terminal.

Examples

2021-01-18