Function export_genomic_coordinates_of_ptm has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring.

Open

    def export_genomic_coordinates_of_ptm(
        self, export_path=None, path=None,
        only_primary_isoforms=False, only_confirmed_mutations=True
    ):
        path = self.choose_path(path)

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File __init__.py has 320 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import gc
import gzip
from abc import abstractmethod
from collections import defaultdict
from typing import List, Iterable

MutationImporter has 27 functions (exceeds 20 allowed). Consider refactoring.

Open

class MutationImporter(BioImporter, MutationExporter):

    @abstract_property
    def name(self):
        """Name of the mutations importer"""

Avoid deeply nested control flow statements.

Open

                        if relevant:
                            protein_mutations.append(protein_mutation)
                            sites_affected.append(mutation_sites)

Avoid deeply nested control flow statements.

Open

                        for site in mutation.get_affected_ptm_sites():
                            relevant_proteome_coordinates.append(
                                (pos, protein, alt, ref, site)
                            )

Avoid deeply nested control flow statements.

Open

                        for pos, protein, alt, ref, site in relevant_proteome_coordinates:
                            if (
                                protein_mutation.startswith(protein.gene_name + ':' + protein.refseq)
                                and
                                protein_mutation.endswith(ref + str(pos) + alt)

Function load has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def load(self, path=None, update=False, **kwargs):
        """Load, parse and insert mutations from given path.

        If update is True, old mutations will be updated and new added.
        Essential difference when using update is that 'update' prevents

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Function look_after_duplicates has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def look_after_duplicates(self, mutation_id, mutations_details, values):
        """To prevent inclusion of duplicate data use this function to check for duplicates
        before adding any data to mutations_details insertion list.

        For example, assuming that clinvar_mutations is an insertion list use:

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