configuration

Options to run MacSyFinder can be specified in a Configuration file. The API described below handles all configuration options for MacSyFinder.

The macsypy.config.MacsyDefaults hold the default values for macsyfinder whereas the macsypy.config.Config hold the values for a macsyfinder run.

Config

class macsypy.config.Config(defaults, parsed_args)[source]

Handle configuration values for macsyfinder. This values come from default and ar superseded by the configuration files, then the command line settings.

__init__(defaults, parsed_args)[source]

Store macsyfinder configuration options and propose an interface to access to them.

The config object is populated with the defaults then superseded with the value specified in configuration files and finally by the options set on the command line.

Parameters
  • defaults (a MacsyDefaults object) –

  • parsed_args (a argspace.Namescape object) – the command line arguments parsed

__weakref__

list of weak references to the object (if defined)

_config_file_2_dict(defaults, files, previous_run=False)[source]

parse config files files, the last one have precedence on the previous on so on, and return a dict with properties, values. The defaults is just used to know the type of the properties and cast them. It is not used to fill the dict with default values.

Parameters
  • defaults (a macsypy.config.MacsyDefaults object) – the macsyfinder defaults value

  • files (list of string) – the configuration files to parse

Returns

dict

_set_db_type(value)[source]

set value for ‘db_type’ option

Parameters

value (str) – the value for db_type, allowed values are : ‘ordered_replicon’, ‘gembase’, ‘unordered’

Raises

ValueError – if value is not allowed

_set_inter_gene_max_space(value)[source]

set value for ‘inter_gene_max_space’ option

Parameters

value (str) – the string parse representing the model fully qualified name and it’s associated value and so on the model_fqn is a string, the associated value must be cast in int

Raises

ValueError – if value is not well formed

_set_max_nb_genes(value)[source]

set value for ‘max_nb_genes’ option

Parameters

value (str) – the string parse representing the model fully qualified name and it’s associated value and so on the model_fqn is a string, the associated value must be cast in int

Raises

ValueError – if value is not well formed

_set_min_genes_required(value)[source]

set value for ‘min_genes_required’ option

Parameters

value (str) – the string parse representing the model fully qualified name and it’s associated value and so on the model_fqn is a string, the associated value must be cast in int

Raises

ValueError – if value is not well formed

_set_min_mandatory_genes_required(value)[source]

set value for ‘min_mandatory_genes_required’ option

Parameters

value (str) – the string parse representing the model fully qualified name and it’s associated value and so on the model_fqn is a string, the associated value must be cast in int

Raises

ValueError – if value is not well formed

_set_models(value)[source]
Parameters

value

The models to search as return by the command line parsing or the configuration files

if value come from command_line

[[‘model1’, ‘def1’, ‘def2’, ‘def3’], [‘model2’, ‘def4’], …]

if value come from config file

[(‘set_1’, ‘T9SS, T3SS, T4SS_typeI’), (‘set_2’, ‘T4P’)] [(model_family, [def_name1, …]), … ]

_set_models_dir(path)[source]
Parameters

path (str) – the path to the models (definitions + profiles) are stored.

_set_multi_loci(value)[source]
Parameters

value (str) – the models fqn list separated by comma of multi loc models

_set_replicon_topology(value)[source]

set the default replicon topology

Parameters

value (str) – ‘circular’ or ‘linear’

_set_sequence_db(path)[source]
Parameters

path (str) – set the path to the sequence file (in fasta format) to analysed

_set_topology_file(path)[source]

test if the path exists and set it in config

Parameters

path (str) – the path to the topology file

_str_2_tuple(value)[source]

transform a string with syntax {model_fqn int} in list of tuple

Parameters

value (str) – the string to parse

Returns

Return type

[(model_fqn, int), ..]

hmmer_dir()[source]
Returns

The name of the directory containing the hmmsearch results (output, error, parsing)

inter_gene_max_space(model_fqn)[source]
Parameters

model_fqn (str) – the model fully qualifed name

Returns

the gene_max_space for the model_fqn or None if it’s does not specify

Return type

int or None

log_level()[source]
Returns

the verbosity output level

Return type

int

max_nb_genes(model_fqn)[source]
Parameters

model_fqn (str) – the model fully qualifed name

Returns

the max_nb_genes for the model_fqn or None if it’s does not specify

Return type

int or None

min_genes_required(model_fqn)[source]
Parameters

model_fqn (str) – the model fully qualifed name

Returns

the min_genes_required for the model_fqn or None if it’s does not specify

Return type

int or None

min_mandatory_genes_required(model_fqn)[source]
Parameters

model_fqn (str) – the model fully qualifed name

Returns

the min_mandatory_genes_required for the model_fqn or None if it’s does not specify

Return type

int or None

multi_loci(model_fqn)[source]
Parameters

model_fqn (str) – the model fully qualified name

Returns

True if the model is multi loci, False otherwise

Return type

bool

out_dir()[source]
Returns

the path to the directory where the results are stored

save(path_or_buf=None)[source]

save itself in a file in ini format.

Note

the undefined options (set to None) are omitted

Parameters

path_or_buf (str or file like object) – where to serialize itself.

working_dir()[source]

alias to config.Config.out_dir()

class macsypy.config.MacsyDefaults(**kwargs)[source]

Handle all default values for macsyfinder. the default values must be defined here, NOT in argument parser nor in config the argument parser or config must use a MacsyDefaults object

__init__(**kwargs)[source]
Parameters

kwargs – allow to overwrite a default value. It mainly used in unit tests

To define a new default value just add an attribute with the default value

__weakref__

list of weak references to the object (if defined)