Index

_

__init__() (macsypy.config.Config method) (macsypy.config.MacsyDefaults method) (macsypy.model_conf_parser.ModelConfParser method) __weakref__ (macsypy.config.Config attribute) (macsypy.config.MacsyDefaults attribute) (macsypy.config.NoneConfig attribute) (macsypy.error.MacsypyError attribute) (macsypy.model_conf_parser.ModelConfParser attribute) _config_file_2_dict() (macsypy.config.Config method) _get_model_conf_node() (macsypy.model_conf_parser.ModelConfParser method) _parse_section() (macsypy.model_conf_parser.ModelConfParser method) _set_command_line_config() (macsypy.config.Config method) _set_db_type() (macsypy.config.Config method) _set_default_config() (macsypy.config.Config method) _set_inter_gene_max_space() (macsypy.config.Config method) _set_log_level() (macsypy.config.Config method) _set_max_nb_genes() (macsypy.config.Config method)

_set_min_genes_required() (macsypy.config.Config method) _set_min_mandatory_genes_required() (macsypy.config.Config method) _set_model_config() (macsypy.config.Config method) _set_models() (macsypy.config.Config method) _set_models_dir() (macsypy.config.Config method) _set_multi_loci() (macsypy.config.Config method) _set_no_cut_ga() (macsypy.config.Config method) _set_options() (macsypy.config.Config method) _set_previous_run_config() (macsypy.config.Config method) _set_project_config_file() (macsypy.config.Config method) _set_replicon_topology() (macsypy.config.Config method) _set_sequence_db() (macsypy.config.Config method) _set_system_models_dir() (macsypy.config.Config method) _set_system_wide_config() (macsypy.config.Config method) _set_topology_file() (macsypy.config.Config method) _set_user_config_file() (macsypy.config.Config method) _set_user_wide_config() (macsypy.config.Config method) _str_2_tuple() (macsypy.config.Config method)

C

CITATION.yml Cluster Config (class in macsypy.config)

CONTRIBUTING CONTRIBUTORS COPYING COPYRIGHT

D

doc

E

EmptyFileError

H

hit_weights() (macsypy.config.Config method)

hmmer_dir() (macsypy.config.Config method)

I

inter_gene_max_space() (macsypy.config.Config method)

L

log_level() (macsypy.config.Config method)

M

MacsydataError MacsyDataLimitError MacsyDefaults (class in macsypy.config) macsypy macsypy.error module macsypy.model_conf_parser module MacsypyError max_nb_genes() (macsypy.config.Config method) min_genes_required() (macsypy.config.Config method)

min_mandatory_genes_required() (macsypy.config.Config method) Model Model family ModelConfParser (class in macsypy.model_conf_parser) ModelDefinition ModelInconsistencyError models_dir() (macsypy.config.Config method) module macsypy.error macsypy.model_conf_parser multi_loci() (macsypy.config.Config method)

N

NoneConfig (class in macsypy.config)

O

OptionError

out_dir() (macsypy.config.Config method)

P

parse() (macsypy.model_conf_parser.ModelConfParser method) parse_filtering() (macsypy.model_conf_parser.ModelConfParser method)

parse_weights() (macsypy.model_conf_parser.ModelConfParser method) pyproject.toml

R

README.md

S

save() (macsypy.config.Config method) setup.cfg setup.py

Solution System SystemDetectionError

T

tests

Timeout

U

utils

W

working_dir() (macsypy.config.Config method)