Uparma - The Universal parameter mapper class in Python

class uparma.uparma.UParma(refresh_jsons=False, source_style='ursgal_style_1')

Universal Parameter Mapper Class

Keyword Arguments:  

• refresh_jsons (bool) – indicates if uparma jsons should be pulled from central repo (https://github.com/uparma/uparma-lib) or not. Note that if jsons are not available in uparma folder, option is overridden and set to True.
• source_style (str) – Convenience when mapper is used to map from the same source style every time, in which case self.convert can be used instead of self.translate

convert(param_dict, target_style=None)

Convenient wrapper to translate params with the source style defined during init.

Calls self.translate with source_style = self.source_style

translate(param_dict, source_style=None, target_style=None)

Translate param_dict from source style into target style.

Keyword Arguments:  

• param_dict (dict) – dict containing parameter and value in a given style
• source_style (str) – style of the input format
• target_style (str) – style to which the parameters should be translated to.

Returns:

dict with the translated key and

values for the input dict with additional information in self.details (see below).

Return type:

translated_params (dict-like)

For example an input in ursgal style:

{
    "precursor_mass_tolerance_unit": "ppm",
    "min_pep_length" : 8
}

can be converted to msgfplus style, yielding:

{
    '-minLength' : 8,
    '-t' : 'ppm'
}

the return object is a dict-like structure which holds additional detailed information accessible via self.details. For the example above, self.details looks like:

{
    'min_pep_length': {
        'source_key': 'min_pep_length',
        'source_style': 'ursgal_style_1',
        'source_value': 8,
        'target_key': '-minLength',
        'target_style': 'msgfplus_style_1',
        'target_value': 8
    },
    'precursor_mass_tolerance_unit': {
        'source_key': 'precursor_mass_tolerance_unit',
       'source_style': 'ursgal_style_1',
       'source_value': 'ppm',
       'target_key': '-t',
       'target_style': 'msgfplus_style_1',
       'target_value': 'ppm'
    }
}