Databases

Basic Usage

dammit handles databases under the dammit databases subcommand. By default, dammit looks for databases in $HOME/.dammit/databases and will install them there if missing. If you have some of the databases already, you can inform dammit with the --database-dir flag.

To check for databases in the default location:

dammit databases

To check for them in a custom location, you can either use the –database-dir flag:

dammit databases --database-dir /path/to/databases

or, you can set the DAMMIT_DB_DIR environment variable. The flag will supersede this variable, falling back to the default if neither is set. For example:

export DAMMIT_DB_DIR=/path/to/databases

This can also be added to your $HOME/.bashrc file to make it persistent.

To download and install them into the default directory:

dammit databases --install

For more details, check out the Advanced-Database-Handling section.

About

dammit uses the following databases:

  1. Pfam-A

    Pfam-A is a collection of protein domain profiles for use with profile hidden markov model programs like hmmer. These searches are moderately fast and very sensitive, and the Pfam database is very well curated. Pfam is used during TransDecoder’s ORF finding and for annotation assignment.

  2. Rfam

    Rfam is a collection of RNA covariance models for use with programs like Infernal. Covariance models describe RNA secondary structure, and Rfam is a curated database of non-coding RNAs.

  3. OrthoDB

    OrthoDB is a curated database of orthologous genes. It attempts to classify proteins from all major groups of eukaryotes and trace them back to their ancestral ortholog.

  4. BUSCO

    BUSCO databases are collections of “core” genes for major domains of life. They are used with an accompanying BUSCO program which assesses the completeness of a genome, transcriptome, or list of genes. There are multiple BUSCO databases, and which one you use depends on your particular organism. Currently available databases are:

    1. Metazoa
    2. Vertebrata
    3. Arthropoda
    4. Eukaryota

    dammit uses the metazoa database by default, but different databases can be used with the --busco-group parameter. You should try to use the database which most closely bounds your organism.

  5. uniref90

    uniref is a curated collection of most known proteins, clustered at a 90% similarity threshold. This database is comprehensive, and thus quite enormous. dammit does not include it by default due to its size, but it can be installed and used with the --full flag.

A command using all of these potential options and databases might look like:

dammit databases --install --database-dir /path/to/dbs --full --busco-group arthropoda

Advanced Database Handling

Several of these databases are quite large. Understandably, you probably don’t want to download or prepare them again if you already have. There are a few scenarios you might run in to.

  1. You already have the databases, and they’re all in one place and properly named.

    Excellent! This is the easiest. You can make use of dammit’s --database-dir flag to tell it where to look. When running with --install, it will find the existing files and prep them if necessary.:

    dammit databases --database-dir <my_database_dir> --install

  2. Same as above, but they have different names.

    dammit expects the databases to be “properly” named – that is, named the same as their original forms. If your databases aren’t named the same, you’ll need to fix them. But that’s okay! We can just soft link them. Let’s say you have Pfam-A already, but for some reason its named all-the-models.hmm. You can link them to the proper name like so:

    cd <my_database_dir>
ln -s all-the-models.hmm Pfam-A.hmm

    If you already formatted it with hmmpress, you can avoid repeating that step as well:

    ln -s all-the-models.hmm.h3f Pfam-A.hmm.h3f
ln -s all-the-models.hmm.h3i Pfam-A.hmm.h3i
ln -s all-the-models.hmm.h3m Pfam-A.hmm.h3m
ln -s all-the-models.hmm.h3p Pfam-A.hmm.h3p

    For a complete listing of the expected names, just run the databases command:

    dammit databases

  3. You have the databases, but they’re scattered to the virtual winds.

    The fix here is similar to the above. This time, however, we’ll soft link all the databases to one location. If you’ve run dammit databases, a new directory will have been created at $HOME/.dammit/databases. This is where they are stored by default, so we might as well use it! For example:

    cd $HOME/.dammit/databases
ln -s /path/to/all-the-models.hmm Pfam-A.hmm

    And repeat for all the databases. Now, in the future, you will be able to run dammit without the –database-dir flag.

Alternatively, if this all seems like too much of a hassle and you have lots of hard drive space, you can just say “to hell with it!” and reinstall everything with:

dammit databases --install