scripts

The are 4 entry points.

  • macsyfinder: which is the main script

  • macsydata: which allow to manage the models (command name msf_data)

  • macsyconfig: an interactive conversational utility to generate macsyfinder configuration file (command name msf_config)

  • macsyprofile: an utility dedicated to modelers which gather information about hmmer output (command name msf_profile)

API reference

macsyfinder

Main entrypoint to macsyfinder

macsyfinder.scripts.msf.alarm_handler(signum: Signals, frame) → None[source]

Handle signal alarm flush loggers :param signum: :param frame: :raise: Timeout

macsyfinder.scripts.msf.list_models(args: Namespace) → str[source]
Parameters:

args – The command line argument once parsed

Returns:

a string representation of all models and submodels installed.

macsyfinder.scripts.msf.main(args: list[str] | None = None, loglevel: Literal['NOTSET', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] | int | None = None)[source]

main entry point to MacSyFinder do some check before to launch main_search_systems() which is the real function that perform a search

Parameters:

  • args – the arguments passed on the command line without the program name

  • loglevel – the output verbosity

macsyfinder.scripts.msf.parse_args(args: list[str]) → tuple[ArgumentParser, Namespace][source]
Parameters:

args – The arguments provided on the command line

Returns:

The arguments parsed

macsydata

wrapper to macsylib.macsydata

macsyconfig

Entrypoint for macsyconfig command which generate a MacSyFinder config file

class macsyfinder.scripts.macsyconfig.ConfigParserWithComments(defaults=None, dict_type=<class 'dict'>, allow_no_value=False, *, delimiters=('=', ':'), comment_prefixes=('#', ';'), inline_comment_prefixes=None, strict=True, empty_lines_in_values=True, default_section='DEFAULT', interpolation=<object object>, converters=<object object>, allow_unnamed_section=False)[source]

Extend ConfigParser to allow comment in serialization

add_comment(section: str, option: str, comment: str, comment_nb: int = count(1), add_space_before: bool = False, add_space_after: bool = True) → None[source]

Write a comment in .ini-format (start line with #)

Parameters:

  • section – the name of the section

  • option – the name of the option

  • comment – the comment linked to this option

  • comment_nb – the identifier of the comment by default an integer

  • add_space_before

  • add_space_after

write(file: IO) → None[source]

Write an .ini-format representation of the configuration state.

Parameters:

file (file) – the file object wher to write the configuration

class macsyfinder.scripts.macsyconfig.Theme(ERROR: str = '\x1b[1m\x1b[31m', WARN: str = '\x1b[33m', SECTION: str = '\x1b[35m', RESET: str = '\x1b[0m', RETRY: str = '\x1b[33m', QUESTION: str = '\x1b[32m', EMPHASIZE: str = '\x1b[1m', EXPLANATION: str = '\x1b[0m', DEFAULT: str = '\x1b[1m\x1b[32m')[source]

Handle color combination to highlight interactive question

__delattr__(name)

Implement delattr(self, name).

__eq__(other)

Return self==value.

__hash__()

Return hash(self).

__init__(ERROR: str = '\x1b[1m\x1b[31m', WARN: str = '\x1b[33m', SECTION: str = '\x1b[35m', RESET: str = '\x1b[0m', RETRY: str = '\x1b[33m', QUESTION: str = '\x1b[32m', EMPHASIZE: str = '\x1b[1m', EXPLANATION: str = '\x1b[0m', DEFAULT: str = '\x1b[1m\x1b[32m') → None
__repr__()

Return repr(self).

__setattr__(name, value)

Implement setattr(self, name, value).

__weakref__

list of weak references to the object

macsyfinder.scripts.macsyconfig._validator(cast_func: Callable, raw: Any, default: Any, sequence: bool = False) → Any[source]
Parameters:

  • cast_func – the function which will cast the raw value

  • raw – the raw value

  • default – the default value

  • sequence – True if the value is a sequence, False otherwise

Returns:

The cast Value

Raises:

MacsypyError – if the raw value cannot be cast

macsyfinder.scripts.macsyconfig.ask(question: str, validator: Callable, default: Any = None, expected: Any = None, explanation: str = '', sequence: bool = False, question_color: str | None = None, retry: int = 2)[source]

ask a question on the terminal and return the user response check if the user response is allowed (right type, among allowed values, …)

Parameters:

  • question – The question to prompt to the user on the terminal

  • validator – what validator to be used to check the user response

  • default – the default value

  • expected – the values allowed (can be a list of value

  • explanation – some explanation about the option

  • sequence – True if the parameter accept a sequence of value (comma separated values)

  • question_color – the color of the question display to the user

  • retry – The number of time to repeat the question if the response is rejected

Returns:

the value casted in right type

macsyfinder.scripts.macsyconfig.check_bool(raw: str, default: bool, expected, sequence: bool = False) → bool[source]

Check if value can be cast in str

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – not used here to have the same signature for all check_xxx functions

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.check_choice(raw: str, default: str, expected: list[str], sequence: bool = False) → str[source]

Check if value is in list of expected values

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – the allowed values for this option

  • sequence – True if parameter accept a sequence of value, False otherwise

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.check_dir(raw: str, default: str, expected, sequence: bool = False) → str[source]

Check if value point to a directory

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – not used here to have the same signature for all check_xxx functions

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.check_exe(raw: str, default: str, expected, sequence: bool = False) → str[source]

Check if value point to an executable

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – not used here to have the same signature for all check_xxx functions

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.check_file(raw: str, default: str, expected, sequence: bool = False) → str[source]

Check if value point to a file

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – not used here to have the same signature for all check_xxx functions

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.check_float(raw: str, default: float, expected, sequence: bool = False) → float[source]

Check if value can be cast in float

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – not used here to have the same signature for all check_xxx functions

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.check_positive_int(raw: str, default: int, expected, sequence: bool = False) → int[source]

Check if value can be cast in integer >=0

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – not used here to have the same signature for all check_xxx functions

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.check_str(raw: str, default: str, expected, sequence: bool = False) → str[source]

Check if value can be cast in str

Parameters:

  • raw – the value return by the user

  • default – the default value for the option

  • expected – not used here to have the same signature for all check_xxx functions

Returns:

value

Raises:

MacsypyError – if the value cannot be cast in right type

macsyfinder.scripts.macsyconfig.epilog(path: str) → str[source]
Returns:

the text to the user before to start the configuration

macsyfinder.scripts.macsyconfig.main(args: list[str] | None = None) → None[source]

The main entrypoint of the script

Parameters:

args – the command line arguments.

macsyfinder.scripts.macsyconfig.parse_args(args: list[str], color: bool = True) → Namespace[source]

parse command line

Parameters:

args – the command line arguments

Returns:

macsyfinder.scripts.macsyconfig.prolog() → str[source]
Returns:

the text displayed to the user when the configuration file is generated

macsyfinder.scripts.macsyconfig.serialize(config: ConfigParserWithComments, path: str) → None[source]

save the configuration on file

Parameters:

  • config – the config to save

  • path (str) – where to store the configuration

macsyfinder.scripts.macsyconfig.set_base_options(config: ConfigParserWithComments, defaults: MacsyDefaults, use_defaults: bool = False) → None[source]

Options for base section

Parameters:

  • config – The config to setup

  • defaults – the macsyfinder defaults values

  • use_defaults (bool) – If True do not ask any question use the defaults values

macsyfinder.scripts.macsyconfig.set_general_options(config: ConfigParserWithComments, defaults: MacsyDefaults, use_defaults: bool = False) → None[source]

Options for general section

Parameters:

  • config – The config to setup

  • defaults – the macsyfinder defaults values

  • use_defaults (bool) – If True do not ask any question use the defaults values

macsyfinder.scripts.macsyconfig.set_hmmer_options(config: ConfigParserWithComments, defaults: MacsyDefaults, use_defaults: bool = False) → None[source]

Options for hmmer section

Parameters:

  • config – The config to setup

  • defaults – the macsyfinder defaults values

  • use_defaults (bool) – If True do not ask any question use the defaults values

macsyfinder.scripts.macsyconfig.set_path_options(config: ConfigParserWithComments, defaults: MacsyDefaults, use_defaults: bool = False) → None[source]

Options for directories section

Parameters:

  • config – The config to setup

  • defaults – the macsyfinder defaults values

  • use_defaults (bool) – If True do not ask any question use the defaults values

macsyfinder.scripts.macsyconfig.set_score_options(config: ConfigParserWithComments, defaults: MacsyDefaults, use_defaults: bool = False) → None[source]

Options for scoring section

Parameters:

  • config – The config to setup

  • defaults – the macsyfinder defaults values

  • use_defaults (bool) – If True do not ask any question use the defaults values

macsyfinder.scripts.macsyconfig.set_section(sec_name: str, options: dict[slice(<class 'str'>, typing.Any, None)], config: ~macsyfinder.scripts.macsyconfig.ConfigParserWithComments, defaults: ~macsylib.config.MacsyDefaults, use_defaults: bool = False) → ConfigParserWithComments[source]

iter over options of a section ask question for each option and set this option in the config

Parameters:

  • sec_name – the name of the section

  • options – a dictionnary with the options to set up for this section

  • config – The config to fill in.

  • defaults – the macsyfinder defaults values

  • use_defaults – The user skip this section so use defaults to set in config object

Returns:

configuration

macsyprofile

wrapper to macsylib.macsyprofile