List installed banks

BeeDeeM comes with an additional tool aims at listing installed banks.

This tool also helps you to locate:

• banks that are available for use with BLAST software

• banks containg annotations

The tool is only available from the command line and is called:

• bdm info -h

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 no arguments. Simply use:

bdm info -d all -f txt

The result is directly dumped in standard output, such as:

BeeDeeM - 5.0.0

Configuration:

  Install path           : /opt/beedeem/
  Master configuration   : /opt/conf/dbms.config
  Log path               : /var/log/
  Work path              : /tmp/
  Bank configuration file: /biobase/dbmirror.config
  Bank repository path   : /biobase/
  Bank repository size   : 361,67 Mb

Installed banks
 - Protein banks: 1
      * SwissProt_human
        Description: Human subset of UniprotKB/SwissProt.
        BLAST+ use: -db /biobase/p/SwissProt_human/current/SwissProt_human/SwissProt_humanM
        Annotated bank: true
        Size (sequences): 20,168
        Size on disk: 361,67 Mb
        Install date: 2017-03-12, 17:55

 - Nucleotide banks: 0

 - Biological classification banks: 0

The 'info' command accepts the following optional arguments:

-d <type-of-repository> -f <format> -u <username>

where:

• "type-of-repository" is one of: n, p, b, all. This allows you to list nucleotide, protein, biological calssifications or all banks, respectively. Default is: all.

• "format" is one of: txt, html, galaxy. Default is: txt.

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

Locate your BLAST banks

Using that utility tool, you can easily identify banks that are available for BLAST. If you have a closer look at the above bank list, you will see this line:

BLAST+ use: -db /biobase/p/SwissProt_human/current/SwissProt_human/SwissProt_humanM

This is the "-db" argument you can use with BLAST+ software to run a BLAST job against that bank.

Locate banks to annotate your BLAST results

In a same way, the above output displays that line:

Annotated bank: true

Which means that the "SwissProt_human" contains annotations: features and biological classifications. So, that bank can be used with the Annotate tool.

Get loc files for Galaxy

You can easily enable Galaxy web platform to use banks installed by BeeDeeM by creating loc files as follows:

# dump nucleotide banks into appropriate loc file
bdm info -f galaxy -d n > blastdb_n.loc

# do the same for protein banks
bdm info -f galaxy -d p > blastdb_p.loc

Such files contains list of banks ready to be used by NCBI BLAST Galaxy wrappers.