# DRAM 1.4.6


{{< admonition tip "Conda" true >}}
See the 'activating the conda environment' section below to access this
software.
{{< /admonition >}}

## DRAM-1.4.6

DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating
metagenomic assembled genomes and
[VirSorter](https://github.com/simroux/VirSorter) identified viral contigs.
DRAM annotates MAGs and viral contigs using [KEGG](https://www.kegg.jp/) (if
provided by the user), [UniRef90](https://www.uniprot.org/),
[PFAM](https://pfam.xfam.org/), [dbCAN](http://bcb.unl.edu/dbCAN2/), [RefSeq
viral](https://www.ncbi.nlm.nih.gov/genome/viruses/),
[VOGDB](http://vogdb.org/) and the [MEROPS](https://www.ebi.ac.uk/merops/)
peptidase database as well as custom user databases. DRAM is run in two
stages. First an annotation step to assign database identifiers to gene, and
then a distill step to curate these annotations into useful functional
categories. Additionally, viral contigs are further analyzed during to
identify potential AMGs. This is done via assigning an auxiliary score and
flags representing the confidence that a gene is both metabolic and viral.

-------------------------------------------------------------------------------

## Activating the conda environment

Check out a node with `qrsh` and run:

```console
bash
source /local/cluster/conda-envs/envs/DRAM-1.4.6/activate.sh
```

### Using conda activate DRAM

If your conda is set up as
[here](https://software.cqls.oregonstate.edu/tips/posts/using-the-system-miniconda-3-install/),
you can run `conda activate DRAM` instead of the `source` line above.

## Running over SGE

To use over SGE, include the source line above in a shell script prior to your
commands, e.g.

```bash
$ cat run_DRAM.sh
#!/usr/bin/env bash
source /local/cluster/conda-envs/envs/DRAM-1.4.6/activate.sh
DRAM.py ...
```

And then run `hqsub 'bash ./run_DRAM.sh' -r sge.DRAM ...`

### Using hqsub --conda

You can also run:

`hqsub 'conda activate DRAM; DRAM.py ...' -r sge.DRAM --conda ...`

Without having to write a separate shell script.

## Location and version

```console
$ which DRAM.py
/local/cluster/conda-envs/envs/DRAM/bin/DRAM.py
$ DRAM-setup.py version
1.4.6
```

## help message

```console
$ DRAM.py -h
usage: DRAM.py [-h]
               {annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations} ...

positional arguments:
  {annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations}
    annotate            Annotate genomes/contigs/bins/MAGs
    annotate_genes      Annotate already called genes, limited functionality compared to
                        annotate
    distill             Summarize metabolic content of annotated genomes
    strainer            Strain annotations down to genes of interest
    neighborhoods       Find neighborhoods around genes of interest
    merge_annotations   Merge multiple annotations to one larger set

options:
  -h, --help            show this help message and exit
```

software ref: <https://github.com/WrightonLabCSU/DRAM>  
software ref: <https://github.com/WrightonLabCSU/DRAM/wiki>
research ref: <https://doi.org/10.1093/nar/gkaa621>