> For the complete documentation index, see [llms.txt](https://rocket-9.gitbook.io/rocket-docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://rocket-9.gitbook.io/rocket-docs/api/rk.msacluster.md).

# rk.msacluster

`rk.msacluster` subsamples sequences from an MSA with DBSCAN and uniform random sampling.

This script is modified from the [AF\_cluster repository](https://github.com/HWaymentSteele/AF_Cluster/blob/main/scripts/ClusterMSA.py).

It writes one `.a3m` file per subsample. It assumes the first sequence in the FASTA or A3M file is the query.

### Options

```
options:
  -h, --help            show this help message and exit
  -i I                  fasta/a3m file of original alignment, or path containing fasta/a3m files
  -o O                  name of output directory to write MSAs to.
  --n_controls N_CONTROLS
                        Number of control msas to generate (Default 10)
  --verbose             Print cluster info as they are generated.
  --scan                Select eps value on 1/4 of data, shuffled.
  --eps_val EPS_VAL     Use single value for eps instead of scanning.
  --resample            If included, will resample the original MSA with replacement before writing.
  --gap_cutoff GAP_CUTOFF
                        Remove sequences with gaps representing more than this frac of seq.
  --min_eps MIN_EPS     Min epsilon value to scan for DBSCAN (Default 3).
  --max_eps MAX_EPS     Max epsilon value to scan for DBSCAN (Default 20).
  --eps_step EPS_STEP   step for epsilon scan for DBSCAN (Default 0.5).
  --min_samples MIN_SAMPLES
                        Default min_samples for DBSCAN (Default 3, recommended no lower than that).
  --run_PCA             Run PCA on one-hot embedding of sequences and store in output_cluster_metadata.tsv
  --run_TSNE            Run TSNE on one-hot embedding of sequences and store in output_cluster_metadata.tsv
```

### Example

```bash
rk.msacluster v1 -i alignments/ -o msaclusters --run_TSNE
```

You can score the resulting subsamples with [rk.score](/rocket-docs/api/rk.score.md).


---

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