cli.rst

Command Line Interface

To run any of the five Snekmer operation modes, simply call:

snekmer {mode}

Each mode has its own mode-specific options and parameters to be specified on the command line or the config.yaml file, respectively.

For an overview of Snekmer usage, reference the help command (snekmer --help).

$ snekmer --help
usage: snekmer [-h] [-v] {cluster,model,search,learn,apply} ...

Snekmer: A tool for kmer-based sequence analysis using amino acid reduction (AAR)

options:
-h, --help            show this help message and exit
-v, --version         print version and exit

mode:
Snekmer mode

{cluster,model,search,learn,apply}

Tailored references for the individual operation modes can be accessed via snekmer {mode} --help.

Configuration

To run Snekmer, create a config.yaml file containing desired parameters. A template is included in the repository. Note that a config file must be included, in the same directory as input directory, for Snekmer to operate.

Snekmer assumes that input files are stored in the input directory, and automatically creates an output directory to save all output files. Snekmer also assumes background files, if any, are stored in input/background. An example of the assumed directory structure is shown below:

Snekmer cluster, model, and search input

.
├── config.yaml
├── input/
│   ├── background/
│   │   ├── X.fasta
│   │   ├── Y.fasta
│   │   └── etc.
│   ├── A.fasta
│   ├── B.fasta
│   └── etc.
├── output/
│   ├── ...
│   └── ...

Snekmer learn input

.
├── config.yaml
├── input/
│   ├── A.fasta # known sequences to "learn" kmer counts matrix from
│   ├── B.fasta # known sequences to "learn" kmer counts matrix from
│   └── etc.
│   └── base/  # optional
│      └── base-kmer-counts.csv # optional file to additively merge kmer counts with
├── annotations/
│   └── annotations.ann # annotation files used for predicting future sequences
├── output/
│   ├── ...
│   └── ...

Snekmer apply input

.
├── config.yaml
├── input/
│   ├── A.fasta # unknown sequences to "apply" kmer counts matrix on
│   ├── B.fasta # unknown sequences to "apply" kmer counts matrix on
│   └── etc.
├── counts/
│   └── kmer-counts-total.csv #kmer counts matrix generated in ``learn``
├── confidence/
│   └── global-confidence-scores.csv #global confidence distribution generated in ``learn``
├── output/
│   ├── ...
│   └── ...

Partial Workflow

To execute only a part of the workflow, the --until option can be invoked. For instance, to execute the workflow only through the kmer vector generation step, run:

snekmer {mode} --until vectorize

All Options

.. argparse::
   :module: snekmer.cli
   :func: get_main_args
   :prog: snekmer