search

MannLabs / alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.
https://mannlabs.github.io/alphapept/
Apache License 2.0
167 stars 29 forks source link

Remove redundancy of filter and score functions in scoring notebook #275

Open ibludau opened 3 years ago

ibludau commented 3 years ago

Is your feature request related to a problem? Please describe. filter_with_xx functions in the scoring notebook are redundant and should be revised.

Describe the solution you'd like Use a single combined function for 'filter_with_xxx' and 'score_xxx'.

Describe alternatives you've considered Call 'filter_with_xxx' within 'score_xxx'.

Additional context The 'filter_with_xxx' functions were introduced with commit: eee2972b19d6ea96156e9c7ea10a99e801dea115 >> 3 Aug 2020 Here, an unused 'fdr_level' parameter was additionally added.

jalew188 commented 3 years ago

In fasta.py,

def get_frag_dict(parsed_pep, mass_dict):
    frag_dict = {}
    frag_masses, frag_type = get_fragmass(parsed_pep, constants.mass_dict)
    ...

the mass_dict argument is never used as well.