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.

configuration API reference

MacsyDefaults

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)

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 This values come from default and ar superseded by the configuration files, then the command line settings.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 in several steps, the rules of precedence are

system wide conf < user home conf < model conf < (project conf | previous run) < command line

system wide conf = etc/macsyfinder/macsyfinder.conf user home conf = ~/.macsyfinder/macsyfinder.conf model conf = model_conf.xml at the root of the model package project conf = macsyfinder.conf where the analysis is run previous run = macsyfinder.conf in previous run results dir command line = 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(file)[source]

Parse a configuration file in ini format in dictionnary

Parameters:: file (str) – path to the configuration file
Returns:: the parsed options
Return type:: dict

_set_command_line_config(parsed_args)[source]

Parameters:: parsed_args (argparse.Namespace object.) – the argument set on the command line

_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_default_config()[source]: set the value comming from MacsyDefaults

_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_log_level(value)[source]

Parameters:: value –
Returns:

_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_model_config(model_conf_path)[source]

Set the options from the model package model_conf.xml file

Parameters:: model_conf_path (str) – The path to the model_conf.xml file

_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’]
if value come from config file: [‘set_1’, ‘T9SS T3SS T4SS_typeI’)] [(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_no_cut_ga(value)[source]

Parameters:: value –
Returns:
Return type:

_set_options(options)[source]

set key, value in the general config

Parameters:: options (a dictionary with option name as keys and values as values) – the options to specify in general config

_set_previous_run_config(prev_config_path)[source]

Set the options specified by the user on the command line via –previous-run

Parameters:: prev_config_path –

_set_project_config_file(config_path)[source]

Set the options from the macsyfinder.conf present in the current directory

Parameters:: config_path (str) – the path to the configuration file

_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_system_models_dir(value)[source]

Parameters:: value (list of string or a single string) – the path of the models dir set by the system (vs set by the user)
Returns:

_set_system_wide_config(config_path)[source]

set the options from the system wide configuration file

Parameters:: config_path (str) –

_set_topology_file(path)[source]

test if the path exists and set it in config

Parameters:: path (str) – the path to the topology file

_set_user_config_file(config_path)[source]

Set the options specified by the user on the command line via the –cfg-file option

Parameters:: config_path (str) – The path to the configuration path

_set_user_wide_config(config_path)[source]

Set the options from the ~/.macsyfinder/macsyfinder.conf file

Parameters:: config_path (str) – The path to the ~/.macsyfinder/macsyfinder.conf

_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), …]

hit_weights()[source]

Returns:: the options used in scoring systems (mandatory_weight, accessory_weight, itself_weight, exchangeable_weight, out_of_cluster_weight)
Return type:: dict

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

models_dir()[source]

Returns:: list of models dir path
Return type:: list of str

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()

NoneConfig

class macsypy.config.NoneConfig[source]

Minimalist Config object just use in some special case wher config is require by api but not used for instance in macsypy.package.Package

__weakref__: list of weak references to the object (if defined)