MacSyFinder relies on the definition of models of macromolecular systems as a set of models’ components to be searched by similarity search, and a set of rules regarding their genomic organization and their requirement level to make a complete system (mandatory, accessory components, number of components required).
A MacSyFinder model (macsy-model for short) is the association of several elements:
The models are grouped by family possibly gathering sub-families (multiple levels allowed), for instance Secretion, Cas-proteins…
A set of models from a same family (coherent set) of systems to detect is called hereafter a macsy-model package
NEW in V2.
For details on how to create your own macsy-models, have a look at the Modeller Guide.
How to install new models
MacSyFinder does not provide models. You must install models before using it.
macsydata utility tool is shipped with MacSyFinder to deal with macsy-models:
macsydata <subcommand> [options]
The main sub-commands are
macsydata availableto get the list of macsy-models available
macsydata searchto search a model given its name or a pattern in its description
macsydata installto install a macsy-model package (the installed version can be set see –help)
macsydata citeto retrieve information on how to cite the model
macsydata definitionto display one or a set of model defintion
macsydata --helpto get the extended list of available subcommands
macsydata <subcommand> --helpto get help about the specified subcommand
NEW in V2
Where the models are located
MacSyFinder looks at several locations to find macsy-models.
By default macsydata installs models in a shared location (set by –install-data option) that is /usr/share/macsyfinder/ or /usr/local/share/macsyfinder depending on your Operating System distribution. If you use a virtualenv, the shared resources are located in the <virtualenv>/share/macsyfinder directory.
If you don’t own rights to install system-wide, you can install models in the MacSyFinder’s cache located in your home: $HOME/.macsyfinder/data/. macsydata installs packages in this location when you use the –user option. The packages installed in user land is added to the system-wide packages.
If two packages have the same name, the package in the user land supersedes the system-wide package.
If you cannot install macsy-model packages in system or user land locations, you can install models in specific directory with the –target option.
macsydata install –target <my_models>
The specify this specific location with the
--models-dir command-line option.
macsyfinder –db-type ordered_replicon –models-dir=my_models –models TFF-SF all –sequence-db my_genome.fasta
The path must point at a directory that contains macsy-model packages as described above.