scripts¶
The are 4 entry points.
macsyfinder: which is the main scripts
macsydata: which allow to manage the models
macsyconfig: an interactive conversational utility to generate macsyfinder configuration file
macsyprofile: an utility dedicated to modelers which gather information about hmmer output
API reference¶
macsyfinder¶
Main entrypoint to macsyfinder
-
macsypy.scripts.macsyfinder.
_loner_warning
(systems)[source]¶ - Parameters
systems – sequence of systems
- Returns
warning for loner which have less occurrences than systems occurrences in which this lone is used except if the loner is also multi system
- Return type
list of string
-
macsypy.scripts.macsyfinder.
_outfile_header
(models_fam_name, models_version)[source]¶ - Returns
The 2 first lines of each result file
- Return type
str
-
macsypy.scripts.macsyfinder.
_search_in_ordered_replicon
(hits_by_replicon, models_to_detect, config, logger)[source]¶ - Parameters
hits_by_replicon –
models_to_detect –
config –
logger –
- Returns
-
macsypy.scripts.macsyfinder.
_search_in_unordered_replicon
(hits_by_replicon, models_to_detect, logger)[source]¶ - Parameters
hits_by_replicon –
models_to_detect –
logger –
- Returns
-
macsypy.scripts.macsyfinder.
get_version_message
()[source]¶ - Returns
the long description of the macsyfinder version
- Return type
str
-
macsypy.scripts.macsyfinder.
likely_systems_to_tsv
(models_fam_name, models_version, likely_systems, hit_system_tracker, sys_file)[source]¶ print likely systems occurrences (from unordered replicon) in a file in tabulated separeted value (tsv) format
- Parameters
likely_systems (list of
macsypy.system.LikelySystem
objects) – list of systems foundhit_system_tracker (
macsypy.system.HitSystemTracker
object) – a filled HitSystemTracker.sys_file (file object) – The file where to write down the systems occurrences
- Returns
None
-
macsypy.scripts.macsyfinder.
likely_systems_to_txt
(models_fam_name, models_version, likely_systems, hit_system_tracker, sys_file)[source]¶ print likely systems occurrences (from unordered replicon) in a file in text human readable format :param likely_systems: list of systems found :type likely_systems: list of
macsypy.system.LikelySystem
objects :param hit_system_tracker: a filled HitSystemTracker. :type hit_system_tracker:macsypy.system.HitSystemTracker
object :param sys_file: file object :return: None
-
macsypy.scripts.macsyfinder.
list_models
(args)[source]¶ - Parameters
args (
argparse.Namespace
object) – The command line argument once parsed- Returns
a string representation of all models and submodels installed.
- Return type
str
-
macsypy.scripts.macsyfinder.
loners_to_tsv
(models_fam_name, models_version, systems, sys_file)[source]¶ get loners from valid systems and save them on file
- Parameters
systems (list of
macsypy.system.System
object) – the systems from which the loners are extractsys_file (file object open in write mode) – the file where loners are saved
-
macsypy.scripts.macsyfinder.
main
(args=None, loglevel=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 (List of string) – the arguments passed on the command line without the program name
loglevel (a positive int or a string among 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL') – the output verbosity
-
macsypy.scripts.macsyfinder.
multisystems_to_tsv
(models_fam_name, models_version, systems, sys_file)[source]¶ get multisystems from valid systems and save them on file
- Parameters
systems (list of
macsypy.system.System
object) – the systems from which the loners are extractsys_file (file object open in write mode) – the file where multisystems are saved
-
macsypy.scripts.macsyfinder.
parse_args
(args)[source]¶ - Parameters
args (List of strings [without the program name]) – The arguments provided on the command line
- Returns
The arguments parsed
- Return type
aprgparse.Namespace
object.
-
macsypy.scripts.macsyfinder.
rejected_candidates_to_tsv
(models_fam_name, models_version, rejected_candidates, cand_file)[source]¶
-
macsypy.scripts.macsyfinder.
rejected_candidates_to_txt
(models_fam_name, models_version, rejected_candidates, cand_file)[source]¶ print rejected clusters in a file
- Parameters
rejected_candidates (list of
macsypy.system.RejectedCandidate
objects) – list of candidates which does not contitute a systemcand_file (file object) – The file where to write down the rejected candidates
- Returns
None
-
macsypy.scripts.macsyfinder.
search_systems
(config, model_registry, models_def_to_detect, logger)[source]¶ Do the job, this function is the orchestrator of all the macsyfinder mechanics at the end several files are produced containing the results
macsyfinder.conf: The set of variables used to runt this job
macsyfinder.systems: The list of the potential systems
- macsyfinder.rejected_cluster: The list of all clusters and clustrs combination
which has been rejected and the reason
macsyfinder.log: the copy of the standard output
- Parameters
config (
macsypy.config.Config
object) – The MacSyFinder Configurationmodel_registry (
macsypy.registries.ModelRegistry
object) – the registry of all modelsmodels_def_to_detect (list of
macsypy.registries.DefinitionLocation
objects) – the defintions to detectlogger (
colorlog.Logger
object) – The logger use to display information to the user. It must be initialized. seemacsypy.init_logger()
- Returns
the systems and rejected clusters found
- Return type
([
macsypy.system.System
, …], [macsypy.cluster.RejectedCAndidate
, …])
-
macsypy.scripts.macsyfinder.
solutions_to_tsv
(models_fam_name, models_version, solutions, hit_system_tracker, sys_file)[source]¶ print solution in a file in tabulated format A solution is a set of systems which represents an optimal combination of systems to maximize the score.
- Parameters
solutions (list of list of
macsypy.system.System
objects) – list of systems foundhit_system_tracker (
macsypy.system.HitSystemTracker
object) – a filled HitSystemTracker.sys_file (file object) – The file where to write down the systems occurrences
- Returns
None
-
macsypy.scripts.macsyfinder.
summary_best_solution
(models_fam_name, models_version, best_solution_path, sys_file, models_fqn, replicon_names)[source]¶ do a summary of best_solution in best_solution_path and write it on out_path a summary compute the number of system occurrence for each model and each replicon .. code-block:: text
replicon model_fqn_1 model_fqn_2 …. rep_name_1 1 2 rep_name_2 2 0
columns are separated by character
- Parameters
best_solution_path (str) – the path to the best_solution file in tsv format
sys_file – the file where to save the summary
models_fqn (list of string) – the fully qualified names of the models
replicon_names (list of string) – the name of the replicons used
-
macsypy.scripts.macsyfinder.
systems_to_tsv
(models_fam_name, models_version, systems, hit_system_tracker, sys_file)[source]¶ print systems occurrences in a file in tabulated format
- Parameters
systems (list of
macsypy.system.System
objects) – list of systems foundhit_system_tracker (
macsypy.system.HitSystemTracker
object) – a filled HitSystemTracker.sys_file (file object) – The file where to write down the systems occurrences
- Returns
None
-
macsypy.scripts.macsyfinder.
systems_to_txt
(models_fam_name, models_version, systems, hit_system_tracker, sys_file)[source]¶ print systems occurrences in a file in human readable format
- Parameters
systems (list of
macsypy.system.System
objects) – list of systems foundhit_system_tracker (
macsypy.system.HitSystemTracker
object) – a filled HitSystemTracker.sys_file (file object) – The file where to write down the systems occurrences
- Returns
None
-
macsypy.scripts.macsyfinder.
unlikely_systems_to_txt
(models_fam_name, models_version, unlikely_systems, sys_file)[source]¶ print hits (from unordered replicon) which probably does not make a system occurrences in a file in human readable format
- Parameters
unlikely_systems – list of
macsypy.system.UnLikelySystem
objectssys_file (file object) – The file where to write down the systems occurrences
- Returns
None
macsydata¶
This is the entrypoint to the macsydata command macsydata allow the user to manage the MacSyFinder models
-
macsypy.scripts.macsydata.
_find_all_installed_packages
(models_dir=None) → macsypy.registries.ModelRegistry[source]¶ - Returns
all models installed
-
macsypy.scripts.macsydata.
_find_installed_package
(pack_name, models_dir=None) → Optional[macsypy.registries.ModelLocation][source]¶ search if a package names pack_name is already installed
- Parameters
pack_name – the name of the family model to search
- Returns
The model location corresponding to the pack_name
- Return type
-
macsypy.scripts.macsydata.
_search_in_desc
(pattern: str, remote: macsypy.package.RemoteModelIndex, packages: List[str], match_case: bool = False)[source]¶ - Parameters
pattern – the substring to search packages descriptions
remote – the uri of the macsy-models index
packages – list of packages to search in
match_case – True if the search is case sensitive, False otherwise
- Returns
-
macsypy.scripts.macsydata.
_search_in_pack_name
(pattern: str, remote: macsypy.package.RemoteModelIndex, packages: List[str], match_case: bool = False) → List[Tuple[str, str, Dict]][source]¶ - Parameters
pattern – the substring to search packages names
remote – the uri of the macsy-models index
packages – list of packages to search in
match_case – True if the search is case sensitive, False otherwise
- Returns
-
macsypy.scripts.macsydata.
build_arg_parser
() → argparse.ArgumentParser[source]¶ Build argument parser.
- Return type
argparse.ArgumentParser
object
-
macsypy.scripts.macsydata.
cmd_name
(args: argparse.Namespace) → str[source]¶ Return the name of the command being executed (scriptname + operation).
- Example
macsydata uninstall
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
str
-
macsypy.scripts.macsydata.
do_available
(args: argparse.Namespace) → None[source]¶ List Models available on macsy-models :param args: the arguments passed on the command line :return: None
-
macsypy.scripts.macsydata.
do_check
(args: argparse.Namespace) → None[source]¶ - Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_cite
(args: argparse.Namespace) → None[source]¶ How to cite an installed model.
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_download
(args: argparse.Namespace) → str[source]¶ Download tarball from remote models repository.
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_freeze
(args: argparse.Namespace) → None[source]¶ display all models installed with there respective version, in requirement format.
-
macsypy.scripts.macsydata.
do_help
(args: argparse.Namespace) → None[source]¶ Display on stdout the content of readme file if the readme file does nopt exists display a message to the user see
macsypy.package.help()
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line (the package name)- Returns
None
- Raises
ValueError – if the package name is not known.
-
macsypy.scripts.macsydata.
do_info
(args: argparse.Namespace) → None[source]¶ Show information about installed model.
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_install
(args: argparse.Namespace) → None[source]¶ Install new models in macsyfinder local models repository.
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_list
(args: argparse.Namespace) → None[source]¶ List installed models.
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_search
(args: argparse.Namespace) → None[source]¶ Search macsy-models for Model in a remote index. by default search in package name, if option -S is set search also in description by default the search is case insensitive except if option –match-case is set.
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_show_definition
(args: argparse.Namespace) → None[source]¶ display on stdout the definition if only a package or sub-package is specified display all model definitions in the corresponding package or subpackage
for instance
TXSS+/bacterial T6SSii T6SSiii
display models TXSS+/bacterial/T6SSii and TXSS+/bacterial/T6SSiii
TXSS+/bacterial all or TXSS+/bacterial
display all models contains in TXSS+/bacterial subpackage
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
do_uninstall
(args: argparse.Namespace) → None[source]¶ Remove models from macsyfinder local models repository.
- Parameters
args (
argparse.Namespace
object) – the arguments passed on the command line- Return type
None
-
macsypy.scripts.macsydata.
get_version_message
()[source]¶ - Returns
the long description of the macsyfinder version
- Return type
str
-
macsypy.scripts.macsydata.
init_logger
(level='INFO', out=True)[source]¶ - Parameters
level – The logger threshold could be a positive int or string among: ‘CRITICAL’, ‘ERROR’, ‘WARNING’, ‘INFO’, ‘DEBUG’
out – if the log message must be displayed
- Returns
logger
- Return type
logging.Logger
instance
macsyconfig¶
Entrypoint for macsyconfig command which generate a MacSyFinder config file
-
class
macsypy.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>)[source]¶ Extend ConfigParser to allow comment in serialization
-
add_comment
(section, option, comment, comment_nb=count(1), add_space_before=False, add_space_after=True)[source]¶ Write a comment in .ini-format (start line with #)
- Parameters
section – the name of the sction
option (str) – the name of the option
comment (str) – the comment linked to this option
comment_nb (int) – the identifier of the comment by default an integer
add_space_before (bool) –
add_space_after (bool) –
-
-
class
macsypy.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 hylight interactive question
-
__weakref__
¶ list of weak references to the object (if defined)
-
-
macsypy.scripts.macsyconfig.
ask
(question, validator, default=None, expected=None, explanation='', sequence=False, question_color=None, retry=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 (str) – The question to prompt to the user on the terminal
validator (a function define in this module starting by check_) – 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 (str) – some explanation about the option
sequence (bool) – True if the parameter accept a sequence of value (comma separated values)
question_color (an attribute of
macsypy.scripts.macsyconfig.Theme
) – the color of the question display to the userretry (int) – The number of time to repeat the question if the response is rejected
- Returns
the value casted in right type
-
macsypy.scripts.macsyconfig.
check_bool
(raw, default, expected, sequence=False)[source]¶ Check if value can be cast in str
- Parameters
raw (str) – the value return by the user
default (str) – 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
-
macsypy.scripts.macsyconfig.
check_choice
(raw, default, expected, sequence=False)[source]¶ Check if value is in list of expected values
- Parameters
raw (str) – the value return by the user
default (str) – the default value for the option
expected – the allowed vlaues for this option
- Returns
value
- Raises
MacsypyError – if the value cannot be cast in right type
-
macsypy.scripts.macsyconfig.
check_dir
(raw, default, expected, sequence=False)[source]¶ Check if value point to a directory
- Parameters
raw (str) – the value return by the user
default (str) – 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
-
macsypy.scripts.macsyconfig.
check_exe
(raw, default, expected, sequence=False)[source]¶ Check if value point to an executable
- Parameters
raw (str) – the value return by the user
default (str) – 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
-
macsypy.scripts.macsyconfig.
check_file
(raw, default, expected, sequence=False)[source]¶ Check if value point to a file
- Parameters
raw (str) – the value return by the user
default (str) – 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
-
macsypy.scripts.macsyconfig.
check_float
(raw, default, expected, sequence=False)[source]¶ Check if value can be cast in float
- Parameters
raw (str) – the value return by the user
default (float) – 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
-
macsypy.scripts.macsyconfig.
check_positive_int
(raw, default, expected, sequence=False)[source]¶ Check if value can be cast in integer >=0
- Parameters
raw (str) – the value return by the user
default (int) – 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
-
macsypy.scripts.macsyconfig.
check_str
(raw, default, expected, sequence=False)[source]¶ Check if value can be cast in str
- Parameters
raw (str) – the value return by the user
default (str) – 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
-
macsypy.scripts.macsyconfig.
epilog
(path)[source]¶ return the text to the user before to start the configuration
-
macsypy.scripts.macsyconfig.
main
(args=None) → None[source]¶ The main entrypoint of the script
- Parameters
args –
-
macsypy.scripts.macsyconfig.
parse_args
(args)[source]¶ parse command line
- Parameters
args (list of string) – the command line arguments
- Returns
- Return type
argparse.Namespace
object
-
macsypy.scripts.macsyconfig.
prolog
()[source]¶ return the text displayed to the user when the configuration file is generated
-
macsypy.scripts.macsyconfig.
serialize
(config, path)[source]¶ save the configuration on file
- Parameters
config (
ConfigParserWithComments
object) – the config to savepath (str) – where to store the configuration
-
macsypy.scripts.macsyconfig.
set_base_options
(config, defaults, use_defaults=False)[source]¶ Options for base section
- Parameters
config (
ConfigParserWithComments
object) – The config to setupdefaults (
macsypy.config.MacsyDefaults
object) – the macsyfinder defaults valuesuse_defaults (bool) – If True do not ask any question use the defaults values
-
macsypy.scripts.macsyconfig.
set_general_options
(config, defaults, use_defaults=False)[source]¶ Options for general section
- Parameters
config (
ConfigParserWithComments
object) – The config to setupdefaults (
macsypy.config.MacsyDefaults
object) – the macsyfinder defaults valuesuse_defaults (bool) – If True do not ask any question use the defaults values
-
macsypy.scripts.macsyconfig.
set_hmmer_options
(config, defaults, use_defaults=False)[source]¶ Options for hmmer section
- Parameters
config (
ConfigParserWithComments
object) – The config to setupdefaults (
macsypy.config.MacsyDefaults
object) – the macsyfinder defaults valuesuse_defaults (bool) – If True do not ask any question use the defaults values
-
macsypy.scripts.macsyconfig.
set_path_options
(config, defaults, use_defaults=False)[source]¶ Options for directories section
- Parameters
config (
ConfigParserWithComments
object) – The config to setupdefaults (
macsypy.config.MacsyDefaults
object) – the macsyfinder defaults valuesuse_defaults (bool) – If True do not ask any question use the defaults values
-
macsypy.scripts.macsyconfig.
set_score_options
(config, defaults, use_defaults=False)[source]¶ Options for scoring section
- Parameters
config (
ConfigParserWithComments
object) – The config to setupdefaults (
macsypy.config.MacsyDefaults
object) – the macsyfinder defaults valuesuse_defaults (bool) – If True do not ask any question use the defaults values
-
macsypy.scripts.macsyconfig.
set_section
(sec_name, options, config, defaults, use_defaults=False)[source]¶ iter over options of a section ask question for each option and set this option in the config
- Parameters
sec_name (str) – the name of the section
options (dict) – a dictionnary with the options to set up for this section
config (
ConfigParserWithComments
object) – The config to fill in.defaults (
macsypy.config.MacsyDefaults
object) – the macsyfinder defaults valuesuse_defaults (bool) – The user skip this section so use defaults to set in config object
- Returns
macsyprofile¶
-
class
macsypy.scripts.macsyprofile.
HmmProfile
(gene_name, gene_profile_lg, hmmer_output, cfg)[source]¶ Handle the HMM output files
-
__init__
(gene_name, gene_profile_lg, hmmer_output, cfg)[source]¶ - Parameters
gene (
macsypy.gene.CoreGene
object) – the gene corresponding to the profile search reported herehmmer_output (string) – The path to the raw Hmmer output file
cfg (
macsypy.config.Config
object) – the configuration object
-
__weakref__
¶ list of weak references to the object (if defined)
-
_build_my_db
(hmm_output: str) → Dict[source]¶ Build the keys of a dictionary object to store sequence identifiers of hits.
- Parameters
hmm_output (string) – the path to the hmmsearch output to parse.
- Returns
a dictionary containing a key for each sequence id of the hits
- Return type
dict
-
_fill_my_db
(macsyfinder_idx: str, db: Dict) → None[source]¶ Fill the dictionary with information on the matched sequences
- Parameters
macsyfinder_idx (string) – the path the macsyfinder index corresponding to the dataset
db (dict) – the database containing all sequence id of the hits.
-
_hit_start
(line: str) → bool[source]¶ - Parameters
line (string) – the line to parse
- Returns
True if it’s the beginning of a new hit in Hmmer raw output files. False otherwise
- Return type
boolean.
-
_parse_hmm_body
(hit_id, gene_profile_lg, seq_lg, coverage_threshold, replicon_name, position_hit, i_evalue_sel, b_grp)[source]¶ Parse the raw Hmmer output to extract the hits, and filter them with threshold criteria selected (“coverage_profile” and “i_evalue_select” command-line parameters)
- Parameters
hit_id (str) – the sequence identifier
gene_profile_lg (int) – the length of the profile matched
coverage_threshold (float) – the minimal coverage of the profile to be reached in the Hmmer alignment for hit selection.
replicon_name (str) – the identifier of the replicon
position_hit (int) – the rank of the sequence matched in the input dataset file
i_evalue_sel (float) – the maximal i-evalue (independent evalue) for hit selection
b_grp (list of list of strings) – the Hmmer output lines to deal with (grouped by hit)
- Paramint seq_lg
the length of the sequence
- Returns
a sequence of hits
- Return type
list of
macsypy.report.CoreHit
objects
-
_parse_hmm_header
(h_grp) → str[source]¶ - Parameters
h_grp (sequence of string (<itertools._grouper object at 0x7ff9912e3b50>)) – the sequence of string return by groupby function representing the header of a hit
- Returns
the sequence identifier from a set of lines that corresponds to a single hit
- Return type
string
-
parse
() → List[macsypy.scripts.macsyprofile.LightHit][source]¶ parse a hmm output file and extract all hits and do some basic computation (coverage profile)
- Returns
The list of extracted hits
-
-
class
macsypy.scripts.macsyprofile.
LightHit
(gene_name: str, id: str, seq_length: int, replicon_name: str, position: int, i_eval: float, score: float, profile_coverage: float, sequence_coverage: float, begin_match: int, end_match: int)[source]¶ Handle hmm hits
-
__weakref__
¶ list of weak references to the object (if defined)
-
-
macsypy.scripts.macsyprofile.
get_gene_name
(path: str, suffix: str) → str[source]¶ - Parameters
path (str) – The path to the hmm output to analyse
suffix (str) – the suffix of the hmm output file
- Returns
the name of the analysed gene
- Return type
str
-
macsypy.scripts.macsyprofile.
get_profile_len
(path: str) → int[source]¶ Parse the HMM profile to extract the length and the presence of GA bit threshold
- Parameters
path (str) – The path to the hmm profile used to produced the hmm search output to analyse
- Returns
the length, presence of ga bit threshold
- Return type
tuple(int length, bool ga_threshold)
-
macsypy.scripts.macsyprofile.
get_version_message
() → str[source]¶ - Returns
the long description of the macsyfinder version
- Return type
str
-
macsypy.scripts.macsyprofile.
header
(cmd: List[str]) → str[source]¶ - Parameters
cmd – the command use dto launch this analyse
- Returns
The header of the result file
-
macsypy.scripts.macsyprofile.
init_logger
(level='INFO', out=True)[source]¶ - Parameters
level – The logger threshold could be a positive int or string among: ‘CRITICAL’, ‘ERROR’, ‘WARNING’, ‘INFO’, ‘DEBUG’
out – if the log message must be displayed
- Returns
logger
- Return type
logging.Logger
instance
-
macsypy.scripts.macsyprofile.
main
(args=None, log_level=None) → None[source]¶ main entry point to macsyprofile
- Parameters
args (List of string) – the arguments passed on the command line without the program name
log_level (a positive int or a string among 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL') – the output verbosity