Py Protein Inference Module

class DataStore(object):
    """
    The following Class serves as the data storage object for a protein inference analysis
    The class serves as a central point that is accessed at virtually every PI processing step


    Attributes:
        main_data_form (list): List of unrestricted Psm objects.
        parameter_file_object (ProteinInferenceParameter): protein inference parameter
            [object][pyproteininference.parameters.ProteinInferenceParameter].
        restricted_peptides (list): List of non flaking peptide strings present in the current analysis.
        main_data_restricted (list): List of restricted [Psm][pyproteininference.physical.Psm] objects.
            Restriction is based on the parameter_file_object and the object is created by function
                [restrict_psm_data][pyproteininference.datastore.DataStore.restrict_psm_data].
        scored_proteins (list): List of scored [Protein][pyproteininference.physical.Protein] objects.
            Output from scoring methods from [scoring][pyproteininference.scoring].
        grouped_scored_proteins (list): List of scored [Protein][pyproteininference.physical.Protein]
            objects that have been grouped and sorted. Output from
                [run_inference][pyproteininference.inference.Inference.run_inference] method.
        scoring_input (list): List of non-scored [Protein][pyproteininference.physical.Protein] objects.
            Output from [create_scoring_input][pyproteininference.datastore.DataStore.create_scoring_input].
        picked_proteins_scored (list): List of [Protein][pyproteininference.physical.Protein] objects that pass
            the protein picker algorithm ([protein_picker][pyproteininference.datastore.DataStore.protein_picker]).
        picked_proteins_removed (list): List of [Protein][pyproteininference.physical.Protein] objects that do not
            pass the protein picker algorithm ([protein_picker][pyproteininference.datastore.DataStore.protein_picker]).
        protein_peptide_dictionary (collections.defaultdict): Dictionary of protein strings (keys) that map to sets
            of peptide strings based on the peptides and proteins found in the search. Protein -> set(Peptides).
        peptide_protein_dictionary (collections.defaultdict): Dictionary of peptide strings (keys) that map to sets
            of protein strings based on the peptides and proteins found in the search. Peptide -> set(Proteins).
        high_low_better (str): Variable that indicates whether a higher or a lower protein score is better.
            This is necessary to sort Protein objects by score properly. Can either be "higher" or "lower".
        psm_score (str): Variable that indicates the [Psm][pyproteininference.physical.Psm]
            score being used in the analysis to generate [Protein][pyproteininference.physical.Protein] scores.
        protein_score (str): String to indicate the protein score method used.
        short_protein_score (str): Short String to indicate the protein score method used.
        protein_group_objects (list): List of scored [ProteinGroup][pyproteininference.physical.ProteinGroup]
            objects that have been grouped and sorted. Output from
             [run_inference][pyproteininference.inference.Inference.run_inference] method.
        decoy_symbol (str): String that is used to differentiate between decoy proteins and target proteins. Ex: "##".
        digest (Digest): [Digest object][pyproteininference.in_silico_digest.Digest].
        SCORE_MAPPER (dict): Dictionary that maps potential scores in input files to internal score names.
        CUSTOM_SCORE_KEY (str): String that indicates a custom score is being used.

    """

    SCORE_MAPPER = {
        "q_value": "qvalue",
        "pep_value": "pepvalue",
        "perc_score": "percscore",
        "score": "percscore",
        "q-value": "qvalue",
        "posterior_error_prob": "pepvalue",
        "posterior_error_probability": "pepvalue",
    }

    CUSTOM_SCORE_KEY = "custom_score"

    HIGHER_PSM_SCORE = "higher"
    LOWER_PSM_SCORE = "lower"

    def __init__(self, reader, digest, validate=True):
        """

        Args:
            reader (Reader): Reader object [Reader][pyproteininference.reader.Reader].
            digest (Digest): Digest object
                [Digest][pyproteininference.in_silico_digest.Digest].
            validate (bool): True/False to indicate if the input data should be validated.

        Example:
            >>> pyproteininference.datastore.DataStore(reader = reader, digest=digest)


        """
        # If the reader class is from a percolator.psms then define main_data_form as reader.psms
        # main_data_form is the starting point for all other analyses
        self._init_validate(reader=reader)

        self.parameter_file_object = reader.parameter_file_object  # Parameter object
        self.main_data_restricted = None  # PSM data post restriction
        self.scored_proteins = []  # List of scored Protein objects
        self.grouped_scored_proteins = []  # List of sorted scored Protein objects
        self.scoring_input = None  # List of non scored Protein objects
        self.picked_proteins_scored = None  # List of Protein objects after picker algorithm
        self.picked_proteins_removed = None  # Protein objects removed via picker
        self.protein_peptide_dictionary = None
        self.peptide_protein_dictionary = None
        self.high_low_better = None  # Variable that indicates whether a higher or lower protein score is better
        self.psm_score = None  # PSM Score used
        self.protein_score = None
        self.short_protein_score = None
        self.protein_group_objects = []  # List of sorted protein group objects
        self.decoy_symbol = self.parameter_file_object.decoy_symbol  # Decoy symbol from parameter file
        self.digest = digest  # Digest object

        # Run Checks and Validations
        if validate:
            self.validate_psm_data()
            self.validate_digest()
            self.check_data_consistency()

        # Run method to fix our parameter object if necessary
        self.parameter_file_object.fix_parameters_from_datastore(data=self)

    def get_sorted_identifiers(self, scored=True):
        """
        Retrieves a sorted list of protein strings present in the analysis.

        Args:
            scored (bool): True/False to indicate if we should return scored or non-scored identifiers.

        Returns:
            list: List of sorted protein identifier strings.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> sorted_proteins = data.get_sorted_identifiers(scored=True)
        """

        if scored:
            self._validate_scored_proteins()
            if self.picked_proteins_scored:
                proteins = set([x.identifier for x in self.picked_proteins_scored])
            else:
                proteins = set([x.identifier for x in self.scored_proteins])
        else:
            self._validate_scoring_input()
            proteins = [x.identifier for x in self.scoring_input]

        all_sp_proteins = set(self.digest.swiss_prot_protein_set)

        our_target_sp_proteins = sorted([x for x in proteins if x in all_sp_proteins and self.decoy_symbol not in x])
        our_decoy_sp_proteins = sorted([x for x in proteins if x in all_sp_proteins and self.decoy_symbol in x])

        our_target_tr_proteins = sorted(
            [x for x in proteins if x not in all_sp_proteins and self.decoy_symbol not in x]
        )
        our_decoy_tr_proteins = sorted([x for x in proteins if x not in all_sp_proteins and self.decoy_symbol in x])

        our_proteins_sorted = (
            our_target_sp_proteins + our_decoy_sp_proteins + our_target_tr_proteins + our_decoy_tr_proteins
        )

        return our_proteins_sorted

    @classmethod
    def sort_protein_group_objects(cls, protein_group_objects, higher_or_lower):
        """
        Class Method to sort a list of [ProteinGroup][pyproteininference.physical.ProteinGroup] objects by
        score and number of peptides.

        Args:
            protein_group_objects (list): list of [ProteinGroup][pyproteininference.physical.ProteinGroup] objects.
            higher_or_lower (str): String to indicate if a "higher" or "lower" protein score is "better".

        Returns:
            list: list of sorted [ProteinGroup][pyproteininference.physical.ProteinGroup] objects.

        Example:
            >>> list_of_group_objects = pyproteininference.datastore.DataStore.sort_protein_group_objects(
            >>>     protein_group_objects=list_of_group_objects, higher_or_lower="higher"
            >>> )
        """
        if higher_or_lower == cls.LOWER_PSM_SCORE:

            protein_group_objects = sorted(
                protein_group_objects,
                key=lambda k: (
                    k.proteins[0].score,
                    -k.proteins[0].num_peptides,
                ),
                reverse=False,
            )
        elif higher_or_lower == cls.HIGHER_PSM_SCORE:

            protein_group_objects = sorted(
                protein_group_objects,
                key=lambda k: (
                    k.proteins[0].score,
                    k.proteins[0].num_peptides,
                ),
                reverse=True,
            )

        return protein_group_objects

    @classmethod
    def sort_protein_objects(cls, grouped_protein_objects, higher_or_lower):
        """
        Class Method to sort a list of [Protein][pyproteininference.physical.Protein] objects by score and number of
        peptides.

        Args:
            grouped_protein_objects (list): list of [Protein][pyproteininference.physical.Protein] objects.
            higher_or_lower (str): String to indicate if a "higher" or "lower" protein score is "better".

        Returns:
            list: list of sorted [Protein][pyproteininference.physical.Protein] objects.

        Example:
            >>> scores_grouped = pyproteininference.datastore.DataStore.sort_protein_objects(
            >>>     grouped_protein_objects=scores_grouped, higher_or_lower="higher"
            >>> )
        """
        if higher_or_lower == cls.LOWER_PSM_SCORE:
            grouped_protein_objects = sorted(
                grouped_protein_objects,
                key=lambda k: (k[0].score, -k[0].num_peptides),
                reverse=False,
            )
        if higher_or_lower == cls.HIGHER_PSM_SCORE:
            grouped_protein_objects = sorted(
                grouped_protein_objects,
                key=lambda k: (k[0].score, k[0].num_peptides),
                reverse=True,
            )
        return grouped_protein_objects

    @classmethod
    def sort_protein_sub_groups(cls, protein_list, higher_or_lower):
        """
        Method to sort protein sub lists.

        Args:
            protein_list (list): List of [Protein][pyproteininference.physical.Protein] objects to be sorted.
            higher_or_lower (str): String to indicate if a "higher" or "lower" protein score is "better".

        Returns:
            list: List of [Protein][pyproteininference.physical.Protein] objects to be sorted by score and number of
            peptides.

        """

        # Sort the groups based on higher or lower indication, secondarily sort the groups based on number of unique
        # peptides
        # We use the index [1:] as we do not wish to sort the lead protein...
        if higher_or_lower == cls.LOWER_PSM_SCORE:
            protein_list[1:] = sorted(
                protein_list[1:],
                key=lambda k: (float(k.score), -float(k.num_peptides)),
                reverse=False,
            )
        if higher_or_lower == cls.HIGHER_PSM_SCORE:
            protein_list[1:] = sorted(
                protein_list[1:],
                key=lambda k: (float(k.score), float(k.num_peptides)),
                reverse=True,
            )

        return protein_list

    def get_psm_data(self):
        """
        Method to retrieve a list of [Psm][pyproteininference.physical.Psm] objects.
        Retrieves restricted data if the data has been restricted or all of the data if the data has
        not been restricted.

        Returns:
            list: list of [Psm][pyproteininference.physical.Psm] objects.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> psm_data = data.get_psm_data()
        """
        if not self.main_data_restricted and not self.main_data_form:
            raise ValueError(
                "Both main_data_restricted and main_data_form variables are empty. Please re-load the DataStore "
                "object with a properly loaded Reader object."
            )

        if self.main_data_restricted:
            psm_data = self.main_data_restricted
        else:
            psm_data = self.main_data_form

        return psm_data

    def get_protein_data(self):
        """
        Method to retrieve a list of [Protein][pyproteininference.physical.Protein] objects.
        Retrieves picked and scored data if the data has been picked and scored or just the scored data if the data has
         not been picked.

        Returns:
            list: list of [Protein][pyproteininference.physical.Protein] objects.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> # Data must ben ran through a pyproteininference.scoring.Score method
            >>> protein_data = data.get_protein_data()
        """

        if self.picked_proteins_scored:
            scored_proteins = self.picked_proteins_scored
        else:
            scored_proteins = self.scored_proteins

        return scored_proteins

    def get_protein_identifiers_from_psm_data(self):
        """
        Method to retrieve a list of lists of all possible protein identifiers from the psm data.

        Returns:
            list: list of lists of protein strings.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> protein_strings = data.get_protein_identifiers_from_psm_data()
        """
        psm_data = self.get_psm_data()

        proteins = [x.possible_proteins for x in psm_data]

        return proteins

    def get_q_values(self):
        """
        Method to retrieve a list of all q values for all PSMs.

        Returns:
            list: list of floats (q values).

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> q = data.get_q_values()
        """
        psm_data = self.get_psm_data()

        q_values = [x.qvalue for x in psm_data]

        return q_values

    def get_pep_values(self):
        """
        Method to retrieve a list of all posterior error probabilities for all PSMs.

        Returns:
            list: list of floats (pep values).

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> pep = data.get_pep_values()
        """
        psm_data = self.get_psm_data()

        pep_values = [x.pepvalue for x in psm_data]

        return pep_values

    def get_protein_information_dictionary(self):
        """
        Method to retrieve a dictionary of scores for each peptide.

        Returns:
            dict: dictionary of scores for each protein.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> protein_dict = data.get_protein_information_dictionary()
        """
        psm_data = self.get_psm_data()

        protein_psm_score_dictionary = collections.defaultdict(list)

        # Loop through all Psms
        for psms in psm_data:
            # Loop through all proteins
            for prots in psms.possible_proteins:
                protein_psm_score_dictionary[prots].append(
                    {
                        "peptide": psms.identifier,
                        "Qvalue": psms.qvalue,
                        "PosteriorErrorProbability": psms.pepvalue,
                        "Percscore": psms.percscore,
                    }
                )

        return protein_psm_score_dictionary

    def restrict_psm_data(self, remove1pep=True):
        """
        Method to restrict the input of [Psm][pyproteininference.physical.Psm]  objects.
        This method is central to the pyproteininference module and is able to restrict the Psm data by:
        Q value, Pep Value, Percolator Score, Peptide Length, and Custom Score Input.
        Restriction values are pulled from
        the [ProteinInferenceParameter][pyproteininference.parameters.ProteinInferenceParameter]
        object.

        This method sets the `main_data_restricted` and `restricted_peptides` Attributes for the DataStore object.

        Args:
            remove1pep (bool): True/False on whether or not to remove PEP values that equal 1 even if other restrictions
                are set to not restrict.

        Returns:
            None:

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> data.restrict_psm_data(remove1pep=True)
        """

        # Validate that we have the main data variable
        self._validate_main_data_form()

        logger.info("Restricting PSM data")

        peptide_length = self.parameter_file_object.restrict_peptide_length
        posterior_error_prob_threshold = self.parameter_file_object.restrict_pep
        q_value_threshold = self.parameter_file_object.restrict_q
        custom_threshold = self.parameter_file_object.restrict_custom

        main_psm_data = self.main_data_form
        logger.info("Length of main data: {}".format(len(self.main_data_form)))
        # If restrict_main_data is called, we automatically discard everything that has a PEP of 1
        if remove1pep and posterior_error_prob_threshold:
            main_psm_data = [x for x in main_psm_data if x.pepvalue != 1]

        # Restrict peptide length and posterior error probability
        if peptide_length and posterior_error_prob_threshold and not q_value_threshold:
            restricted_data = []
            for psms in main_psm_data:
                if len(psms.stripped_peptide) >= peptide_length and psms.pepvalue < float(
                    posterior_error_prob_threshold
                ):
                    restricted_data.append(psms)

        # Restrict peptide length only
        if peptide_length and not posterior_error_prob_threshold and not q_value_threshold:
            restricted_data = []
            for psms in main_psm_data:
                if len(psms.stripped_peptide) >= peptide_length:
                    restricted_data.append(psms)

        # Restrict peptide length, posterior error probability, and qvalue
        if peptide_length and posterior_error_prob_threshold and q_value_threshold:
            restricted_data = []
            for psms in main_psm_data:
                if (
                    len(psms.stripped_peptide) >= peptide_length
                    and psms.pepvalue < float(posterior_error_prob_threshold)
                    and psms.qvalue < float(q_value_threshold)
                ):
                    restricted_data.append(psms)

        # Restrict peptide length and qvalue
        if peptide_length and not posterior_error_prob_threshold and q_value_threshold:
            restricted_data = []
            for psms in main_psm_data:
                if len(psms.stripped_peptide) >= peptide_length and psms.qvalue < float(q_value_threshold):
                    restricted_data.append(psms)

        # Restrict posterior error probability and q value
        if not peptide_length and posterior_error_prob_threshold and q_value_threshold:
            restricted_data = []
            for psms in main_psm_data:
                if psms.pepvalue < float(posterior_error_prob_threshold) and psms.qvalue < float(q_value_threshold):
                    restricted_data.append(psms)

        # Restrict qvalue only
        if not peptide_length and not posterior_error_prob_threshold and q_value_threshold:
            restricted_data = []
            for psms in main_psm_data:
                if psms.qvalue < float(q_value_threshold):
                    restricted_data.append(psms)

        # Restrict posterior error probability only
        if not peptide_length and posterior_error_prob_threshold and not q_value_threshold:
            restricted_data = []
            for psms in main_psm_data:
                if psms.pepvalue < float(posterior_error_prob_threshold):
                    restricted_data.append(psms)

        # Restrict nothing... (only PEP gets restricted - takes everything less than 1)
        if not peptide_length and not posterior_error_prob_threshold and not q_value_threshold:
            restricted_data = main_psm_data

        if custom_threshold:
            custom_restricted = []
            if self.parameter_file_object.psm_score_type == Score.MULTIPLICATIVE_SCORE_TYPE:
                for psms in restricted_data:
                    if psms.custom_score <= custom_threshold:
                        custom_restricted.append(psms)

            if self.parameter_file_object.psm_score_type == Score.ADDITIVE_SCORE_TYPE:
                for psms in restricted_data:
                    if psms.custom_score >= custom_threshold:
                        custom_restricted.append(psms)

            restricted_data = custom_restricted

        self.main_data_restricted = restricted_data

        logger.info("Length of restricted data: {}".format(len(restricted_data)))

        self.restricted_peptides = [x.non_flanking_peptide for x in restricted_data]

    def create_scoring_input(self):
        """
        Method to create the scoring input.
        This method initializes a list of [Protein][pyproteininference.physical.Protein] objects to get them ready
        to be scored by [Score][pyproteininference.scoring.Score] methods.
        This method also takes into account the inference type and aggregates peptides -> proteins accordingly.

        This method sets the `scoring_input` and `score` Attributes for the DataStore object.

        The score selected comes from the protein inference parameter object.

        Returns:
            None:

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> data.create_scoring_input()
        """

        logger.info("Creating Scoring Input")

        psm_data = self.get_psm_data()

        protein_psm_dict = collections.defaultdict(list)

        try:
            score_key = self.SCORE_MAPPER[self.parameter_file_object.psm_score]
        except KeyError:
            score_key = self.CUSTOM_SCORE_KEY

        if self.parameter_file_object.inference_type != Inference.PEPTIDE_CENTRIC:
            # Loop through all Psms
            for psms in psm_data:
                psms.assign_main_score(score=score_key)
                # Loop through all proteins
                for prots in psms.possible_proteins:
                    protein_psm_dict[prots].append(psms)

        else:
            self.peptide_to_protein_dictionary()
            sp_proteins = self.digest.swiss_prot_protein_set
            for psms in psm_data:

                # Assign main score
                psms.assign_main_score(score=score_key)
                protein_set = self.peptide_protein_dictionary[psms.non_flanking_peptide]
                # Sort protein_set by sp-alpha, decoy-sp-alpha, tr-alpha, decoy-tr-alpha
                sorted_protein_list = self.sort_protein_strings(
                    protein_string_list=protein_set,
                    sp_proteins=sp_proteins,
                    decoy_symbol=self.parameter_file_object.decoy_symbol,
                )
                # Restrict the number of identifiers by the value in param file max_identifiers_peptide_centric
                sorted_protein_list = sorted_protein_list[: self.parameter_file_object.max_identifiers_peptide_centric]
                protein_name = ";".join(sorted_protein_list)
                protein_psm_dict[protein_name].append(psms)

        protein_list = []
        for pkey in sorted(protein_psm_dict.keys()):
            protein_object = Protein(identifier=pkey)
            protein_object.psms = protein_psm_dict[pkey]
            protein_object.raw_peptides = set([x.identifier for x in protein_psm_dict[pkey]])
            protein_list.append(protein_object)

        self.psm_score = self.parameter_file_object.psm_score
        self.scoring_input = protein_list

    def protein_to_peptide_dictionary(self):
        """
        Method that returns a map of protein strings to sets of peptide strings and is essentially half
         of a BiPartite graph.
        This method sets the `protein_peptide_dictionary` Attribute for the DataStore object.

        Returns:
            collections.defaultdict: Dictionary of protein strings (keys) that map to sets of peptide strings based
            on the peptides and proteins found in the search. Protein -> set(Peptides).

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> protein_peptide_dict = data.protein_to_peptide_dictionary()
        """
        psm_data = self.get_psm_data()

        res_pep_set = set(self.restricted_peptides)
        default_dict_proteins = collections.defaultdict(set)
        for peptide_objects in psm_data:
            for prots in peptide_objects.possible_proteins:
                cur_peptide = peptide_objects.non_flanking_peptide
                if cur_peptide in res_pep_set:
                    default_dict_proteins[prots].add(cur_peptide)

        self.protein_peptide_dictionary = default_dict_proteins

        return default_dict_proteins

    def peptide_to_protein_dictionary(self):
        """
        Method that returns a map of peptide strings to sets of protein strings and is essentially half of a
        BiPartite graph.
        This method sets the `peptide_protein_dictionary` Attribute for the DataStore object.

        Returns:
            collections.defaultdict: Dictionary of peptide strings (keys) that map to sets of protein strings based
                on the peptides and proteins found in the search. Peptide -> set(Proteins).

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> peptide_protein_dict = data.peptide_to_protein_dictionary()
        """
        psm_data = self.get_psm_data()

        res_pep_set = set(self.restricted_peptides)
        default_dict_peptides = collections.defaultdict(set)
        for peptide_objects in psm_data:
            for prots in peptide_objects.possible_proteins:
                cur_peptide = peptide_objects.non_flanking_peptide
                if cur_peptide in res_pep_set:
                    default_dict_peptides[cur_peptide].add(prots)
                else:
                    pass

        self.peptide_protein_dictionary = default_dict_peptides

        return default_dict_peptides

    def unique_to_leads_peptides(self):
        """
        Method to retrieve peptides that are unique based on the data from the searches
        (Not based on the database digestion).

        Returns:
            set: a Set of peptide strings

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> unique_peps = data.unique_to_leads_peptides()
        """
        if self.grouped_scored_proteins:
            lead_peptides = [list(x[0].peptides) for x in self.grouped_scored_proteins]
            flat_peptides = [item for sublist in lead_peptides for item in sublist]
            counted_peps = collections.Counter(flat_peptides)
            unique_to_leads_peptides = set([x for x in counted_peps if counted_peps[x] == 1])
        else:
            unique_to_leads_peptides = set()

        return unique_to_leads_peptides

    def higher_or_lower(self):
        """
        Method to determine if a higher or lower score is better for a given combination of score input and score type.

        This method sets the `high_low_better` Attribute for the DataStore object.

        This method depends on the output from the Score class to be sorted properly from best to worst score.

        Returns:
            str: String indicating "higher" or "lower" depending on if a higher or lower score is a
                better protein score.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> high_low = data.higher_or_lower()
        """

        if not self.high_low_better:
            logger.info("Determining If a higher or lower score is better based on scored proteins")
            worst_score = self.scored_proteins[-1].score
            best_score = self.scored_proteins[0].score

            if float(best_score) > float(worst_score):
                higher_or_lower = self.HIGHER_PSM_SCORE

            if float(best_score) < float(worst_score):
                higher_or_lower = self.LOWER_PSM_SCORE

            logger.info("best score = {}".format(best_score))
            logger.info("worst score = {}".format(worst_score))

            if best_score == worst_score:
                raise ValueError(
                    "Best and Worst scores were identical, equal to {}. Score type {} produced the error, "
                    "please change psm_score type.".format(best_score, self.psm_score)
                )

            self.high_low_better = higher_or_lower

        else:
            higher_or_lower = self.high_low_better

        return higher_or_lower

    def get_protein_identifiers(self, data_form):
        """
        Method to retrieve the protein string identifiers.

        Args:
            data_form (str): Can be one of the following: "main", "restricted", "picked", "picked_removed".

        Returns:
            list: list of protein identifier strings.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> protein_strings = data.get_protein_identifiers(data_form="main")
        """
        if data_form == "main":
            # All the data (unrestricted)
            data_to_select = self.main_data_form
            prots = [[x.possible_proteins] for x in data_to_select]
            proteins = prots

        if data_form == "restricted":
            # Proteins that pass certain restriction criteria (peptide length, pep, qvalue)
            data_to_select = self.main_data_restricted
            prots = [[x.possible_proteins] for x in data_to_select]
            proteins = prots

        if data_form == "picked":
            # Here we look at proteins that are 'picked' (aka the proteins that beat out their matching target/decoy)
            data_to_select = self.picked_proteins_scored
            prots = [x.identifier for x in data_to_select]
            proteins = prots

        if data_form == "picked_removed":
            # Here we look at the proteins that were removed due to picking (aka the proteins that
            # have a worse score than their target/decoy counterpart)
            data_to_select = self.picked_proteins_removed
            prots = [x.identifier for x in data_to_select]
            proteins = prots

        return proteins

    def get_protein_information(self, protein_string):
        """
        Method to retrieve attributes for a specific scored protein.

        Args:
            protein_string (str): Protein Identifier String.

        Returns:
            list: list of protein attributes.

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> protein_attr = data.get_protein_information(protein_string="RAF1_HUMAN|P04049")
        """
        all_scored_protein_data = self.scored_proteins
        identifiers = [x.identifier for x in all_scored_protein_data]
        protein_scores = [x.score for x in all_scored_protein_data]
        groups = [x.group_identification for x in all_scored_protein_data]
        reviewed = [x.reviewed for x in all_scored_protein_data]
        peptides = [x.peptides for x in all_scored_protein_data]
        # Peptide scores currently broken...
        peptide_scores = [x.peptide_scores for x in all_scored_protein_data]
        picked = [x.picked for x in all_scored_protein_data]
        num_peptides = [x.num_peptides for x in all_scored_protein_data]

        main_index = identifiers.index(protein_string)

        list_structure = [
            [
                "identifier",
                "protein_score",
                "groups",
                "reviewed",
                "peptides",
                "peptide_scores",
                "picked",
                "num_peptides",
            ]
        ]
        list_structure.append([protein_string])
        list_structure[-1].append(protein_scores[main_index])
        list_structure[-1].append(groups[main_index])
        list_structure[-1].append(reviewed[main_index])
        list_structure[-1].append(peptides[main_index])
        list_structure[-1].append(peptide_scores[main_index])
        list_structure[-1].append(picked[main_index])
        list_structure[-1].append(num_peptides[main_index])

        return list_structure

    def exclude_non_distinguishing_peptides(self, protein_subset_type="hard"):
        """
        Method to Exclude peptides that are not distinguishing on either the search or database level.

        The method sets the `scoring_input` and `restricted_peptides` variables for the DataStore object.

        Args:
            protein_subset_type (str): Either "hard" or "soft". Hard will select distinguishing peptides based on
                the database digestion. "soft" will only use peptides identified in the search.

        Returns:
            None:

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> data.exclude_non_distinguishing_peptides(protein_subset_type="hard")
        """

        logger.info("Applying Exclusion Model")

        our_proteins_sorted = self.get_sorted_identifiers(scored=False)

        if protein_subset_type == "hard":
            # Hard protein subsetting defines protein subsets on the digest level (Entire protein is used)
            # This is how Percolator PI does subsetting
            peptides = [self.digest.protein_to_peptide_dictionary[x] for x in our_proteins_sorted]
        elif protein_subset_type == "soft":
            # Soft protein subsetting defines protein subsets on the Peptides identified from the search
            peptides = [set(x.raw_peptides) for x in self.scoring_input]
        else:
            # If neither is dfined we do "hard" exclusion
            peptides = [self.digest.protein_to_peptide_dictionary[x] for x in our_proteins_sorted]

        # Get frozen set of peptides....
        # We will also have a corresponding list of proteins...
        # They will have the same index...
        peptide_sets = [frozenset(e) for e in peptides]
        # Find a way to sort this list of sets...
        # We can sort the sets if we sort proteins from above...
        logger.info("{} number of peptide sets".format(len(peptide_sets)))
        non_subset_peptide_sets = set()
        i = 0
        # Get all peptide sets that are not a subset...
        while peptide_sets:
            i = i + 1
            peptide_set = peptide_sets.pop()
            if any(peptide_set.issubset(s) for s in peptide_sets) or any(
                peptide_set.issubset(s) for s in non_subset_peptide_sets
            ):
                continue
            else:
                non_subset_peptide_sets.add(peptide_set)
            if i % 10000 == 0:
                logger.info("Parsed {} Peptide Sets".format(i))

        logger.info("Parsed {} Peptide Sets".format(i))

        # Get their index from peptides which is the initial list of sets...
        list_of_indeces = []
        for pep_sets in non_subset_peptide_sets:
            ind = peptides.index(pep_sets)
            list_of_indeces.append(ind)

        non_subset_proteins = set([our_proteins_sorted[x] for x in list_of_indeces])

        logger.info("Removing direct subset Proteins from the data")
        # Remove all proteins from scoring input that are a subset of another protein...
        self.scoring_input = [x for x in self.scoring_input if x.identifier in non_subset_proteins]

        logger.info("{} proteins in scoring input after removing subset proteins".format(len(self.scoring_input)))

        # For all the proteins that are not a complete subset of another protein...
        # Get the raw peptides...
        raw_peps = [x.raw_peptides for x in self.scoring_input if x.identifier in non_subset_proteins]

        # Make the raw peptides a flat list
        flat_peptides = [Psm.split_peptide(peptide_string=item) for sublist in raw_peps for item in sublist]

        # Count the number of peptides in this list...
        # This is the number of proteins this peptide maps to....
        counted_peptides = collections.Counter(flat_peptides)

        # If the count is greater than 1... exclude the protein entirely from scoring input... :)
        raw_peps_good = set([x for x in counted_peptides.keys() if counted_peptides[x] <= 1])

        # Alter self.scoring_input by removing psms and peptides that are not in raw_peps_good
        current_score_input = list(self.scoring_input)
        for j in range(len(current_score_input)):
            k = j + 1
            psm_list = []
            new_raw_peptides = []
            current_psms = current_score_input[j].psms
            current_raw_peptides = current_score_input[j].raw_peptides

            for psm_scores in current_psms:
                if psm_scores.non_flanking_peptide in raw_peps_good:
                    psm_list.append(psm_scores)

            for rp in current_raw_peptides:
                if Psm.split_peptide(peptide_string=rp) in raw_peps_good:
                    new_raw_peptides.append(rp)

            current_score_input[j].psms = psm_list
            current_score_input[j].raw_peptides = new_raw_peptides

            if k % 10000 == 0:
                logger.info("Redefined {} Peptide Sets".format(k))

        logger.info("Redefined {} Peptide Sets".format(j))

        filtered_score_input = [x for x in current_score_input if x.psms]

        self.scoring_input = filtered_score_input

        # Recompute the flat peptides
        raw_peps = [x.raw_peptides for x in self.scoring_input if x.identifier in non_subset_proteins]

        # Make the raw peptides a flat list
        new_flat_peptides = set([Psm.split_peptide(peptide_string=item) for sublist in raw_peps for item in sublist])

        self.scoring_input = [x for x in self.scoring_input if x.psms]

        self.restricted_peptides = [x for x in self.restricted_peptides if x in new_flat_peptides]

    def protein_picker(self):
        """
        Method to run the protein picker algorithm.

        Proteins must be scored first with [score_psms][pyproteininference.scoring.Score.score_psms].

        The algorithm will match target and decoy proteins identified from the PSMs from the search.
        If a target and matching decoy is found then target/decoy competition is performed.
        In the Target/Decoy pair the protein with the better score is kept and the one with the worse score is
        discarded from the analysis.

        The method sets the `picked_proteins_scored` and `picked_proteins_removed` variables for
        the DataStore object.

        Returns:
            None:

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> data.protein_picker()
        """

        self._validate_scored_proteins()

        logger.info("Running Protein Picker")

        # Use higher or lower class to determine if a higher protein score or lower protein score is better
        # based on the scoring method used
        higher_or_lower = self.higher_or_lower()
        # Here we determine if a lower or higher score is better
        # Since all input is ordered from best to worst we can do the following

        index_to_remove = []
        # data.scored_proteins is simply a list of Protein objects...
        # Create list of all decoy proteins
        decoy_proteins = [x.identifier for x in self.scored_proteins if self.decoy_symbol in x.identifier]
        # Create a list of all potential matching targets (some of these may not exist in the search)
        matching_targets = [x.replace(self.decoy_symbol, "") for x in decoy_proteins]

        # Create a list of all the proteins from the scored data
        all_proteins = [x.identifier for x in self.scored_proteins]
        logger.info("{} proteins scored".format(len(all_proteins)))

        total_targets = []
        total_decoys = []
        decoys_removed = []
        targets_removed = []
        # Loop over all decoys identified in the search
        logger.info("Picking Proteins...")
        for i in range(len(decoy_proteins)):
            cur_decoy_index = all_proteins.index(decoy_proteins[i])
            cur_decoy_protein_object = self.scored_proteins[cur_decoy_index]
            total_decoys.append(cur_decoy_protein_object.identifier)

            # Try, Except here because the matching target to the decoy may not be a result from the search
            try:
                cur_target_index = all_proteins.index(matching_targets[i])
                cur_target_protein_object = self.scored_proteins[cur_target_index]
                total_targets.append(cur_target_protein_object.identifier)

                if higher_or_lower == self.HIGHER_PSM_SCORE:
                    if cur_target_protein_object.score > cur_decoy_protein_object.score:
                        index_to_remove.append(cur_decoy_index)
                        decoys_removed.append(cur_decoy_index)
                        cur_target_protein_object.picked = True
                        cur_decoy_protein_object.picked = False
                    else:
                        index_to_remove.append(cur_target_index)
                        targets_removed.append(cur_target_index)
                        cur_decoy_protein_object.picked = True
                        cur_target_protein_object.picked = False

                if higher_or_lower == self.LOWER_PSM_SCORE:
                    if cur_target_protein_object.score < cur_decoy_protein_object.score:
                        index_to_remove.append(cur_decoy_index)
                        decoys_removed.append(cur_decoy_index)
                        cur_target_protein_object.picked = True
                        cur_decoy_protein_object.picked = False
                    else:
                        index_to_remove.append(cur_target_index)
                        targets_removed.append(cur_target_index)
                        cur_decoy_protein_object.picked = True
                        cur_target_protein_object.picked = False
            except ValueError:
                pass

        logger.info("{} total decoy proteins".format(len(total_decoys)))
        logger.info("{} matching target proteins also found in search".format(len(total_targets)))
        logger.info("{} decoy proteins to be removed".format(len(decoys_removed)))
        logger.info("{} target proteins to be removed".format(len(targets_removed)))

        logger.info("Removing Lower Scoring Proteins...")
        picked_list = []
        removed_proteins = []
        for protein_objects in self.scored_proteins:
            if protein_objects.picked:
                picked_list.append(protein_objects)
            else:
                removed_proteins.append(protein_objects)
        self.picked_proteins_scored = picked_list
        self.picked_proteins_removed = removed_proteins
        logger.info("Finished Removing Proteins")

    def calculate_q_values(self, regular=True):
        """
        Method calculates Q values FDR on the lead protein in the group on the `protein_group_objects`
        instance variable.
        FDR is calculated As (2*decoys)/total if regular is set to True and is
        (decoys)/total if regular is set to False.

        This method updates the `protein_group_objects` for the DataStore object by updating
        the q_value variable of the [ProteinGroup][pyproteininference.physical.ProteinGroup] objects.

        Returns:
            None:

        Example:
            >>> data = pyproteininference.datastore.DataStore(reader = reader, digest=digest)
            >>> # Data must be scored first
            >>> data.calculate_q_values()
        """

        self._validate_protein_group_objects()

        logger.info("Calculating Q values from the protein group objects")

        # pick out the lead scoring protein for each group... lead score is at 0 position
        lead_score = [x.proteins[0] for x in self.protein_group_objects]
        # Now pick out only the lead protein identifiers
        lead_proteins = [x.identifier for x in lead_score]

        lead_proteins.reverse()

        logger.info("Calculating FDRs")
        fdr_list = []
        for i in range(len(lead_proteins)):
            binary_decoy_target_list = [1 if self.decoy_symbol in elem else 0 for elem in lead_proteins]
            total = len(lead_proteins)
            decoys = sum(binary_decoy_target_list)
            # Calculate FDR at every step starting with the entire list...
            # Delete first entry (worst score) every time we go through a cycle
            if regular:
                fdr = (2 * decoys) / (float(total))
            else:
                fdr = (decoys) / (float(total))
            fdr_list.append(fdr)
            del lead_proteins[0]

        qvalue_list = []
        new_fdr_list = []
        logger.info("Calculating Q Values")
        for fdrs in fdr_list:
            new_fdr_list.append(fdrs)
            qvalue = min(new_fdr_list)
            # qvalue = fdrs
            qvalue_list.append(qvalue)

        qvalue_list.reverse()

        logger.info("Assigning Q Values")
        for k in range(len(self.protein_group_objects)):
            self.protein_group_objects[k].q_value = qvalue_list[k]

        fdr_restricted = [x for x in self.protein_group_objects if x.q_value <= self.parameter_file_object.fdr]

        fdr_restricted_set = [self.grouped_scored_proteins[x] for x in range(len(fdr_restricted))]

        onehitwonders = []
        for groups in fdr_restricted_set:
            if int(groups[0].num_peptides) == 1:
                onehitwonders.append(groups[0])

        logger.info(
            "Protein Group leads that pass with more than 1 PSM with a {} FDR = {}".format(
                self.parameter_file_object.fdr,
                str(len(fdr_restricted_set) - len(onehitwonders)),
            )
        )
        logger.info(
            "Protein Group lead One hit Wonders that pass {} FDR = {}".format(
                self.parameter_file_object.fdr, len(onehitwonders)
            )
        )

        logger.info(
            "Number of Protein groups that pass a {} percent FDR: {}".format(
                str(self.parameter_file_object.fdr * 100), len(fdr_restricted_set)
            )
        )

        logger.info("Finished Q value Calculation")

    def validate_psm_data(self):
        """
        Method that validates the PSM data.
        """
        self._validate_decoys_from_data()
        self._validate_isoform_from_data()

    def validate_digest(self):
        """
        Method that validates the [Digest object][pyproteininference.in_silico_digest.Digest].
        """
        self._validate_reviewed_v_unreviewed()
        self._check_target_decoy_split()

    def check_data_consistency(self):
        """
        Method that checks for data consistency.
        """
        self._check_data_digest_overlap_psms()
        self._check_data_digest_overlap_proteins()

    def _check_data_digest_overlap_psms(self):
        """
        Method that logs the overlap between the digested fasta file and the input files on the PSM level.
        """
        peptides = [x.stripped_peptide for x in self.main_data_form]
        peptides_in_digest = set(self.digest.peptide_to_protein_dictionary.keys())
        peptides_from_search_in_digest = [x for x in peptides if x in peptides_in_digest]
        percentage = float(len(set(peptides))) / float(len(set(peptides_from_search_in_digest)))
        logger.info("{} PSMs identified from input files".format(len(peptides)))
        logger.info(
            "{} PSMs identified from input files that are also present in database digestion".format(
                len(peptides_from_search_in_digest)
            )
        )
        logger.info(
            "{}; ratio of PSMs identified from input files to those that are present in the search"
            " and in the database digestion".format(percentage)
        )

    def _check_data_digest_overlap_proteins(self):
        """
        Method that logs the overlap between the digested fasta file and the input files on the Protein level.
        """
        proteins = [x.possible_proteins for x in self.main_data_form]
        flat_proteins = set([item for sublist in proteins for item in sublist])
        proteins_in_digest = set(self.digest.protein_to_peptide_dictionary.keys())
        proteins_from_search_in_digest = [x for x in flat_proteins if x in proteins_in_digest]
        percentage = float(len(flat_proteins)) / float(len(proteins_from_search_in_digest))
        logger.info("{} proteins identified from input files".format(len(flat_proteins)))
        logger.info(
            "{} proteins identified from input files that are also present in database digestion".format(
                len(proteins_from_search_in_digest)
            )
        )
        logger.info(
            "{}; ratio of proteins identified from input files that are also present in database digestion".format(
                percentage
            )
        )

    def _check_target_decoy_split(self):
        """
        Method that logs the number of target and decoy proteins from the digest.
        """
        # Check the number of targets vs the number of decoys from the digest
        targets = [
            x
            for x in self.digest.protein_to_peptide_dictionary.keys()
            if self.parameter_file_object.decoy_symbol not in x
        ]
        decoys = [
            x for x in self.digest.protein_to_peptide_dictionary.keys() if self.parameter_file_object.decoy_symbol in x
        ]
        ratio = float(len(targets)) / float(len(decoys))
        logger.info("Number of Target Proteins in Digest: {}".format(len(targets)))
        logger.info("Number of Decoy Proteins in Digest: {}".format(len(decoys)))
        logger.info("Ratio of Targets Proteins to Decoy Proteins: {}".format(ratio))

    def _validate_decoys_from_data(self):
        """
        Method that checks to make sure that target and decoy proteins exist in the data files.
        """
        # Check to see if we find decoys from our input files
        proteins = [x.possible_proteins for x in self.main_data_form]
        flat_proteins = set([item for sublist in proteins for item in sublist])
        targets = [x for x in flat_proteins if self.parameter_file_object.decoy_symbol not in x]
        decoys = [x for x in flat_proteins if self.parameter_file_object.decoy_symbol in x]
        logger.info("Number of Target Proteins in Data Files: {}".format(len(targets)))
        logger.info("Number of Decoy Proteins in Data Files: {}".format(len(decoys)))

    def _validate_isoform_from_data(self):
        """
        Method that validates whether or not isoforms are able to be identified in the data files.
        """
        # Check to see if we find any proteins with isoform info in name in our input files
        proteins = [x.possible_proteins for x in self.main_data_form]
        flat_proteins = set([item for sublist in proteins for item in sublist])
        if self.parameter_file_object.isoform_symbol:
            non_iso = [x for x in flat_proteins if self.parameter_file_object.isoform_symbol not in x]

        else:
            non_iso = [x for x in flat_proteins]

        if self.parameter_file_object.isoform_symbol:
            iso = [x for x in flat_proteins if self.parameter_file_object.isoform_symbol in x]

        else:
            iso = []
        logger.info("Number of Non Isoform Labeled Proteins in Data Files: {}".format(len(non_iso)))
        logger.info("Number of Isoform Labeled Proteins in Data Files: {}".format(len(iso)))

    def _validate_reviewed_v_unreviewed(self):
        """
        Method that logs whether or not we can distinguish from reviewed and unreviewd protein identifiers
        in the digest.
        """
        # Check to see if we get reviewed prots in digest...
        reviewed_proteins = len(self.digest.swiss_prot_protein_set)
        proteins_in_digest = len(set(self.digest.protein_to_peptide_dictionary.keys()))
        unreviewed_proteins = proteins_in_digest - reviewed_proteins
        logger.info("Number of Total Proteins in from Digest: {}".format(proteins_in_digest))
        logger.info("Number of Reviewed Proteins in from Digest: {}".format(reviewed_proteins))
        logger.info("Number of Unreviewed Proteins in from Digest: {}".format(unreviewed_proteins))

    @classmethod
    def sort_protein_strings(cls, protein_string_list, sp_proteins, decoy_symbol):
        """
        Method that sorts protein strings in the following order: Target Reviewed, Decoy Reviewed, Target Unreviewed,
         Decoy Unreviewed.

        Args:
            protein_string_list (list): List of Protein Strings.
            sp_proteins (set): Set of Reviewed Protein Strings.
            decoy_symbol (str): Symbol to denote a decoy protein identifier IE "##".

        Returns:
            list: List of sorted protein strings.

        Example:
            >>> list_of_group_objects = datastore.DataStore.sort_protein_strings(
            >>>     protein_string_list=protein_string_list, sp_proteins=sp_proteins, decoy_symbol="##"
            >>> )
        """

        our_target_sp_proteins = sorted([x for x in protein_string_list if x in sp_proteins and decoy_symbol not in x])
        our_decoy_sp_proteins = sorted([x for x in protein_string_list if x in sp_proteins and decoy_symbol in x])

        our_target_tr_proteins = sorted(
            [x for x in protein_string_list if x not in sp_proteins and decoy_symbol not in x]
        )
        our_decoy_tr_proteins = sorted([x for x in protein_string_list if x not in sp_proteins and decoy_symbol in x])

        identifiers_sorted = (
            our_target_sp_proteins + our_decoy_sp_proteins + our_target_tr_proteins + our_decoy_tr_proteins
        )

        return identifiers_sorted

    def input_has_q(self):
        """
        Method that checks to see if the input data has q values.
        """
        len_q = len([x.qvalue for x in self.main_data_form if x.qvalue])
        len_all = len(self.main_data_form)
        if len_q == len_all:
            status = True
            logger.info("Input has Q value; Can restrict by Q value")
        else:
            status = False
            logger.warning("Input does not have Q value; Cannot restrict by Q value")

        return status

    def input_has_pep(self):
        """
        Method that checks to see if the input data has pep values.
        """
        len_pep = len([x.pepvalue for x in self.main_data_form if x.pepvalue])
        len_all = len(self.main_data_form)
        if len_pep == len_all:
            status = True
            logger.info("Input has Pep value; Can restrict by Pep value")
        else:
            status = False
            logger.warning("Input does not have Pep value; Cannot restrict by Pep value")

        return status

    def input_has_custom(self):
        """
        Method that checks to see if the input data has custom score values.
        """
        len_c = len([x.custom_score for x in self.main_data_form if x.custom_score])
        len_all = len(self.main_data_form)
        if len_c == len_all:
            status = True
            logger.info("Input has Custom value; Can restrict by Custom value")

        else:
            status = False
            logger.warning("Input does not have Custom value; Cannot restrict by Custom value")

        return status

    def get_protein_objects(self, false_discovery_rate=None, fdr_restricted=False):
        """
        Method retrieves protein objects. Either retrieves FDR restricted list of protien objects,
        or retrieves all objects.

        Args:
            fdr_restricted (bool): True/False on whether to restrict the list of objects based on FDR.

        Returns:
            list: List of scored [ProteinGroup][pyproteininference.physical.ProteinGroup] objects
                that have been grouped and sorted.

        """
        if not false_discovery_rate:
            false_discovery_rate = self.parameter_file_object.fdr
        if fdr_restricted:
            protein_objects = [x.proteins for x in self.protein_group_objects if x.q_value <= false_discovery_rate]
        else:
            protein_objects = self.grouped_scored_proteins

        return protein_objects

    def _init_validate(self, reader):
        """
        Internal Method that checks to make sure the reader object is properly loaded and validated.
        """
        if reader.psms:
            self.main_data_form = reader.psms  # Unrestricted PSM data
            self.restricted_peptides = [x.non_flanking_peptide for x in self.main_data_form]
        else:
            raise ValueError(
                "Psms variable from Reader object is either empty or does not exist. "
                "Make sure your files contain proper data and that you run the 'read_psms' "
                "method on your Reader object."
            )

    def _validate_main_data_form(self):
        """
        Internal Method that checks to make sure the Main data has been defined to run DataStore methods.
        """
        if self.main_data_form:
            pass
        else:
            raise ValueError(
                "Main Data is not defined, thus method cannot be ran. Please make sure PSM data is properly"
                " loaded from the Reader object"
            )

    def _validate_main_data_restricted(self):
        """
        Internal Method that checks to make sure the Main data Restricted has been defined to run DataStore methods.
        """
        if self.main_data_restricted:
            pass
        else:
            raise ValueError(
                "Main Data Restricted is not defined, thus method cannot be ran. Please make sure PSM data is properly"
                " loaded from the Reader object and make sure to run DataStore method 'restrict_psm_data'."
            )

    def _validate_scored_proteins(self):
        """
        Internal Method that checks to make sure that proteins have been scored to run certain subsequent methods.
        """
        if self.picked_proteins_scored or self.scored_proteins:
            pass
        else:
            raise ValueError(
                "Proteins have not been scored, Please initialize a Score object and run a score method with"
                " 'score_psms' instance method."
            )

    def _validate_scoring_input(self):
        """
        Internal Method that checks to make sure that Scoring Input has been created to be able to run scoring methods.
        """
        if self.scoring_input:
            pass
        else:
            raise ValueError(
                "Scoring input has not been created, Please run 'create_scoring_input' method from the DataStore "
                "object to continue."
            )

    def _validate_protein_group_objects(self):
        """
        Internal Method that checks to make sure inference has been run before proceeding.
        """
        if self.protein_group_objects and self.grouped_scored_proteins:
            pass
        else:
            raise ValueError(
                "Either 'protein_group_objects' or 'grouped_scored_proteins' or both DataStore variables are undefined."
                " Please make sure you run an inference method from the Inference class before proceeding."
            )

    def generate_fdr_vs_target_hits(self, fdr_max=0.2):
        """
        Method for calculating FDR vs number of Target Proteins.

        Args:
            fdr_max (float): The maximum false discovery rate to calculate target hits for.
                Will stop once fdr_max is reached.

        Returns:
            list: List of lists of: (FDR, Number of Target Hits). Ordered by increasing number of Target Hits.

        """
        fdr_vs_count = []
        count_list = []
        for pg in self.protein_group_objects:
            if self.decoy_symbol not in pg.proteins[0].identifier:
                count_list.append(pg)
            fdr_vs_count.append([pg.q_value, len(count_list)])

        fdr_vs_count = [x for x in fdr_vs_count if x[0] < fdr_max]

        return fdr_vs_count

    def recover_mapping(self):
        logger.info("Recovering Proteins that exist in the input files but not in the database digest.")
        all_psms = self.get_psm_data()
        proteins = [x.possible_proteins for x in all_psms]
        flat_proteins = [item for sublist in proteins for item in sublist]

        missing_prots = []
        for prot in flat_proteins:
            try:
                self.digest.protein_to_peptide_dictionary[prot]
            except KeyError:
                missing_prots.append(prot)

                psm_data = self.get_psm_data()
                peptides = [x.stripped_peptide for x in psm_data if prot in x.possible_proteins]
                for pep in peptides:
                    self.digest.peptide_to_protein_dictionary.setdefault(pep, set()).add(prot)
                    self.digest.protein_to_peptide_dictionary.setdefault(prot, set()).add(pep)
        if missing_prots:
            logger.info(
                "{} proteins not found in mapping objects, please double check that your database"
                " provided is accurate for the given input data.".format(len(missing_prots))
            )
        else:
            logger.info("No missing proteins in the mapping objects.")