from alphastats.loader.BaseLoader import BaseLoader
import pandas as pd
# Philosopher
# class name needs to be discussed whether MSFragger/Fragpipe/Philospher
[docs]class FragPipeLoader(BaseLoader):
"""Loader for FragPipe-Philosopheroutputfiles
https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#combined_proteintsv
"""
def __init__(
self,
file,
intensity_column="[sample] MaxLFQ Intensity ",
index_column="Protein",
gene_names_column="Gene Names",
confidence_column="Protein Probability",
sep="\t",
**kwargs
):
super().__init__(file, intensity_column, index_column, sep)
if gene_names_column in self.rawinput.columns.to_list():
self.gene_names = gene_names_column
self.confidence_column = confidence_column
self.software = "MSFragger_Philosopher"
"""
- find way to deal with Indistinguishable Proteins, combine ProteinIDs?
"""
# https://github.com/Nesvilab/MSFragger/wiki/Interpreting-MSFragger-Output
# SAMPLE
# columm Spectrum
# https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#combined_proteintsv
# Frag pipe
# https://github.com/Nesvilab/philosopher/wiki/Combined-protein-reports
# ProteinProphet: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5863791/