> For the complete documentation index, see [llms.txt](https://pgdurand.gitbook.io/beedeem/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://pgdurand.gitbook.io/beedeem/utils/cmdline-query.md).

# 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](/beedeem/installation/directory_structure.md) 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](/beedeem/installation/test_install/query-the-bank-repository.md).

You can control `bdm query` tool with some environment variables as stated [in this section](/beedeem/getting-started/beedeem-configuration.md).&#x20;