Annotate (chamois annotate)

usage: chamois annotate [-h] -i INPUT [-H HMM] [--disentangle] [--cds] -o
                        OUTPUT

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 sequence annotations in HDF5 format.