Explain (chamois explain)#

usage: chamois explain [-h] [-m MODEL] {class,feature,cluster} ...

Named Arguments#

-m, --model

The path to an alternative model to extract weights from.

Sub-commands#

class#

Explain which domains contribute to a class prediction.

chamois explain class [-h] [--nonzero | --min-weight MIN_WEIGHT] [-o OUTPUT]
                      [--render]
                      class_id

Positional Arguments#

class_id

The class to explain

Weights#

Control which weights are displayed in the output.

--nonzero

Display non-zero weights instead of only positive weights.

Default: False

--min-weight

The minimum weight to filter the table with.

Default: 0.0

Output#

Mandatory and optional outputs.

-o, --output

The path where to write the cluster contribution table in TSV format.

--render

Display the cluster contribution table in the console.

Default: False

feature#

Explain which features contribute to a class prediction.

chamois explain feature [-h] [--nonzero | --min-weight MIN_WEIGHT] [-o OUTPUT]
                        [--render]
                        feature_id

Positional Arguments#

feature_id

The feature to explain

Weights#

Control which weights are displayed in the output.

--nonzero

Display non-zero weights instead of only positive weights.

Default: False

--min-weight

The minimum weight to filter the table with.

Default: 0.0

Output#

Mandatory and optional outputs.

-o, --output

The path where to write the cluster contribution table in TSV format.

--render

Display the cluster contribution table in the console.

Default: False

cluster#

Explain which genes of a cluster contribute to which predicted classes.

chamois explain cluster [-h] -i INPUT [-H HMM] [--disentangle] [--cds]
                        [-o OUTPUT] [--render]
                        [cluster_id]

Positional Arguments#

cluster_id

The cluster to explain

Input#

Mandatory input files required by the command.

-i, --input

The input BGC sequences to process.

-H, --hmm

The path to the HMM file containing protein domains for annotation.

--disentangle

Remove overlapping domains by best P-value.

Default: False

Gene Finding#

Parameters for controlling gene extraction from clusters.

--cds

Use CDS features in the GenBank input as genes instead of running Pyrodigal.

Default: False

Output#

Mandatory and optional outputs.

-o, --output

The path where to write the cluster contribution table in TSV format.

--render

Display the cluster contribution table in the console.

Default: False