Source code for alphabase.protein.protein_level_decoy

import pandas as pd

from alphabase.protein.fasta import SpecLibFasta
from alphabase.spectral_library.decoy import SpecLibDecoy




class ProteinReverseDecoy(SpecLibDecoy):


    def __init__(self, target_lib: SpecLibFasta):
        self.target_lib = target_lib
        self._precursor_df: pd.DataFrame = pd.DataFrame()
        self.protein_df = pd.DataFrame()
        self.decoy_tag = "REV_"


    def _add_tag_to_a_column_in_protein_df(self, column: str):
        if column in self.protein_df.columns:
            self.protein_df[column] = self.decoy_tag + self.protein_df[column]

    def _make_empty_loc_for_target_protein_df(self):
        self.protein_df = pd.concat(
            [
                pd.DataFrame({"sequence": [""] * len(self.target_lib.protein_df)}),
                self.protein_df,
            ],
            ignore_index=True,
        ).fillna("")

    def _decoy_protein_df(self):
        self.protein_df = self.target_lib.protein_df.copy()
        self.protein_df["sequence"] = self.protein_df.sequence.str[::-1]
        self._add_tag_to_a_column_in_protein_df("protein_id")
        self._add_tag_to_a_column_in_protein_df("full_name")
        self._add_tag_to_a_column_in_protein_df("gene_name")
        self._make_empty_loc_for_target_protein_df()

    def _generate_decoy_sequences(self):
        _target_prot_df = self.target_lib.protein_df
        _target_pep_df = self.target_lib.precursor_df
        self.target_lib.get_peptides_from_protein_df(self.protein_df)
        self._precursor_df = self.target_lib.precursor_df
        self.target_lib.protein_df = _target_prot_df
        self.target_lib._precursor_df = _target_pep_df



    def decoy_sequence(self):
        if (
            not hasattr(self.target_lib, "protein_df")
            or len(self.target_lib.protein_df) == 0
        ):
            return

        self._decoy_protein_df()
        self._generate_decoy_sequences()
        self._remove_target_seqs()




    def append_to_target_lib(self):
        if (
            not hasattr(self.target_lib, "protein_df")
            or len(self.target_lib.protein_df) == 0
        ):
            return
        super().append_to_target_lib()
        self._append_protein_df_to_target_lib()


    def _append_protein_df_to_target_lib(self):
        self.protein_df["decoy"] = 1
        self.target_lib.protein_df["decoy"] = 0
        self.target_lib.protein_df = pd.concat(
            [
                self.target_lib.protein_df,
                self.protein_df.loc[len(self.target_lib.protein_df) :],
            ]
        )



# remove "protein_reverse" decoy due to conflicting with DecoyGenerator,
# as DecoyGenerator only works for peptide-level, but ProteinReverseDecoy
# is protein-level.
# def register_decoy():
#     decoy_lib_provider.register("protein_reverse", ProteinReverseDecoy)