PANORAMA – Model Translation Guide#

The model translation module in PANORAMA allows you to convert system detection models from other tools into the PANORAMA format. Also, it will prepare all required input files, so they can be used directly for annotation and analysis in PANORAMA.

Supported Sources

  • PADLOC (e.g., antiviral defense systems),

  • MacSyFinder-based tools like:

    • DefenseFinder (e.g., restriction-modification, retrons, etc.),

    • CASFINDER ()

    • CONJScan (conjugative systems),

    • TXSScan (type secretion systems),

    • TFFScan (type IV pili),

When should you use it?#

Important

Translated and updated versions of models are already available here.

  1. When a new version exists, and it’s not yet available on PANORAMA models,

  2. When you want to use a specif version, not available on PANORAMA models

  3. When you have your own version of models that use the same grammar as supported sources.

What do you need?#

You should have:

Tool/Source

HMM profiles

models

metadata

PADLOC

Hidden Markov Model profiles (.hmm)

Models in YAML format (.yaml)

File containing HMM information (.txt)

MacSyModel (or like)

Hidden Markov Model profiles (.hmm)

Models in XML format (.xml)

How to run it?#

Use the command line interface (CLI):

panorama utils \
--translate /path/to/models_directory \
--source name_of_the_source \
--output /path/to/output_directory \
--binary \
--hmm_coverage 0.6 \
--target_coverage 0.8

Key options#

Parameter

Type

Description

--translate

Required

The folder with PADLOC, DefenseFinder or MacSyFinder models.

--source

Required

One of the following: padloc, defense-finder, CONJScan, TXSScan, TFFscan.

--output

Required

Where you want PANORAMA to save its output.

--binary

Optional

Use this to speed up annotations (recommended).

--hmm_coverage

Optional

Thresholds for alignment coverage on HMM

--target_coverage

Optional

Thresholds for alignment coverage on target.

Tip

Defense Finder and PADLOC use different threshold for the HMM and the target coverage. Defense Finder use 0.4 for HMM and 0 for target for all profiles. PADLOC define in the metadata a specific threshold for each profile. This default behavior is tunable with the --hmm_coverage and --target_coverage options that will affect a threshold for all profiles.

What files are created?#

After translation, you’ll get:

  • models/: All models in PANORAMA .json format,

  • models_list.tsv: A list of all translated models,

  • hmm/: All HMM profile compatible with the hmm_list TSV file, binary or not,

  • hmm_list.tsv: A list of all hmm with the metadata needed for the annotation.

These files can be used directly in PANORAMA commands.

Example#

Translate PADLOC#

git clone https://github.com/padlocbio/padloc-db.git
mkdir padloc_translate
panorama utils \
--translate padloc-db/ \
--source padloc \
--output padloc_translate/ \
--binary

Tip

PANORAMA automatically find all required files on its own, as the structure is already known.

Translate DefenseFinder#

git clone https://github.com/mdmparis/defense-finder-models.git
mkdir dfinder_translate
panorama utils \
--translate defense-finder-models/ \
--source defense-finder \
--output dfinder_translate/ \
--binary

Note

Defense Finder team as the tendency to reorganize the repository. If you’re trying to translate a new version this could not work. In this case report an issue here