Query databank repository

BeeDeeM comes with an additional tool aims at querying databanks repository by entity ID. Such an ID can be either a sequence ID or an ontology ID.

That tool is only available from the command line.

Note: during script execution, there is nothing displayed on the terminal whether something goes OK or wrong. However, BeeDeeM logs all its work in a dedicated log file located in ${workingDir}. Refer to Directory structure for more information.

Command-line use

Command line takes three arguments, in this order:

bdm query -d <database> -i <seq_id> -f <format> -o <output>

and the result is directly dumped in standard output.

• database [required]: type of repository to query. One of: n, p, d. When using d, use one of: d:taxon, d:EC, d:GO, d:CDD or d:InterPro. When using d:taxon, entry ID can be either a TaxID or a Taxonomy Name (e.g. organism, phylum, etc.). In latter case, Query Tool will dump Taxonomy path;

• seq_id [required]: either a single entry ID, a comma separated list of entry IDs of a path to a file of entry IDs. When using a file of IDs, provide a single ID per line;

• format [required]: output format. One of: txt, fas, html, insd, finsd. When using dico repository type, txt format only applies.

• output [optional]: output file to save results of query. Optional, default is stdout.

Sample use case.

You can control bdm query tool with some environment variables as stated in this section.