minorg.parse_config module

class minorg.parse_config.Lookup(name=None, alias_description='alias', value_description='value', param_set=None, param_sets=None, param_alias=None, param_inpt=None, config_sets: Optional[str] = None, config_aliases=None, fname_set=None, none=None, multikey=True, multiline=True, inverse=False, **parse_kwargs)[source]

Bases: object

__init__(name=None, alias_description='alias', value_description='value', param_set=None, param_sets=None, param_alias=None, param_inpt=None, config_sets: Optional[str] = None, config_aliases=None, fname_set=None, none=None, multikey=True, multiline=True, inverse=False, **parse_kwargs)[source]
fname()[source]
lookup(k, none=None)[source]
lookup_inv(k, none=None)[source]
parse_from_file(fname=None)[source]
parse_from_string(s)[source]
print(header=None, inv=False, prepend=None)[source]
class minorg.parse_config.OptionParams[source]

Bases: object

__init__()[source]
class minorg.parse_config.Param(default, *names, false_true=('False', 'True'), show_any_default=True, description=None, alias_value_description=None, help_subcmd={}, **kwargs)[source]

Bases: object

__init__(default, *names, false_true=('False', 'True'), show_any_default=True, description=None, alias_value_description=None, help_subcmd={}, **kwargs)[source]
custom_default()[source]
format_log(val)[source]
help(subcmd=None)[source]
property long[source]
property short[source]
class minorg.parse_config.Params(config_file)[source]

Bases: object

__init__(config_file)[source]
get_param(param)[source]
parse_attr_mod(s: str)[source]
parse_domain(s: str)[source]
class minorg.parse_config.SetCoverAlgo(value)[source]

Bases: str, enum.Enum

An enumeration.

greedy = 'greedy'[source]
lar = 'LAR'[source]
minorg.parse_config.find_executable(default, *alts)[source]
minorg.parse_config.get_val_default(val, default=None, coerce=None)[source]

If val is empty (None or empty iterable), return default.

minorg.parse_config.get_val_none(val, d: dict, none=None)[source]

Attempt to retrieve value of key-value pair in ‘d’ if val in d.keys(). Failing that, if val is not ‘’ (empty string), return val. Else, return None

minorg.parse_config.inverse_dict(d: dict)[source]

Converts {<k1>:<v1>, <k2>:<v1>, <k3>:<v2>} into {<v1>:[<k1>,<k2>], <v2>:[<k3>]}

minorg.parse_config.mv_dir_overwrite(src_dir, dst_dir, rm_dir=True, ignore=[])[source]
minorg.parse_config.parse_attr_mod_sdict(s: str, attr_sep: str = ',', feature_sep: str = ';', fa_sep: str = ':', alias_sep: str = '=')[source]

Parse attribute modifications from string to dictionary.

Parameters
  • s (str) – required, string of attribute modifications in format ‘<feature type>:<standard attribute field name>=<nonstandard attribute field name>,<standard attribute field name>=<nonstandard attribute field name>;<feature type>:<standard attribute field name>=<nonstandard attribute field name>’ (e.g. ‘mRNA:Parent=Locus_id’)

  • attr_sep (str) – delimiter for attribute modifications of same feature type (default=’,’)

  • feature_sep (str) – delimiter for feature types (default=’;’)

  • fa_sep (str) – delimiter between feature type and attribute modifications (default=’:’)

  • alias_sep (str) – delimiter between standard attribute field name and non-standard attribute field name (default=’=’)

Returns

parsed attribute modifications in format

{<feature>: {<standard attribute field name>: <nonstandard attribute field name>}}

Return type

dict

minorg.parse_config.parse_multiline_inv_sdict(s: str, v_sep: str = ',', **kwargs)[source]

Converts raw ‘<key>:<v1>,<v2>,…,<v5>’ string into {‘<v1>’:’<key>’,’<v2>’:’<key>’, …,’<v5>’:’<key>’} dict.

minorg.parse_config.parse_multiline_multikey_sdict(s: str, k_sep: str = ';', **kwargs)[source]
minorg.parse_config.parse_multiline_sdict(s: str, kv_sep: str = ':')[source]

Converts raw ‘<key1><kv_sep><v1>,<v2>,…,<v5>

<key2><kv_sep><v6>,…,<v9>’ string into

{‘<key1>’:’<v1>,<v2>,…,<v5>’, ‘<key2>’:’<v6>,…,<v9>’} dict.

minorg.parse_config.parse_sep_sdict(s: str, item_sep: str = ';', kv_sep=':')[source]

Converts raw ‘<key1><kv_sep><v1>,<v2>,…,<v5><item_sep><key2><kv_sep><v6>,…,<v9>’ string into {‘<key1>’:’<v1>,<v2>,…,<v5>’, ‘<key2>’:’<v6>,…,<v9>’} dict.