Function gather_ptm_muts_impacts has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

Open

def gather_ptm_muts_impacts(
    source: MutationSource,
    site_type: SiteType,
    limit_to_genes: List[str] = None,
    occurrences=True,

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Function init has 66 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        init: function(new_config)
        {
            configure(new_config)

            box = $(config.box)

Function advanced_searchbar_templator has 66 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function advanced_searchbar_templator(mutation_template, protein_template)
{

    function template_mutation(result, name)
    {

Function CSS_Zoom has 64 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    var CSS_Zoom = function(my_parent)
    {
        var parent = my_parent
        var canvas_size = [];

Function Orbits has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

var Orbits = function ()
{
    var nodes = null
    var central_node = null

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Function source_specific_nucleotide_mappings has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

def source_specific_nucleotide_mappings() -> TableChunk:
    from database import bdb
    from genomic_mappings import decode_csv
    from models import Mutation
    from tqdm import tqdm

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Function prepare_motifs_plot has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

def prepare_motifs_plot(counts_by_gene, site_type: SiteType, y_axis: str):

    # order by percentage
    genes_ordered = genes_by_ratio(counts_by_gene, y_axis)

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Function map_sites_by_sequence has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def map_sites_by_sequence(self, sites: DataFrame) -> DataFrame:
        """Given a site with an isoform it should occur in,
        verify if the site really appears on the given position
        in this isoform and find where in all other isoforms
        this site appears (by exact match of a sequence span,

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Mutation has 22 functions (exceeds 20 allowed). Consider refactoring.

Open

class Mutation(BioModel, MutatedMotifs):
    __table_args__ = (
        db.Index('mutation_index', 'alt', 'protein_id', 'position'),
        db.UniqueConstraint('alt', 'protein_id', 'position')
    )

Function scores_for_proteins has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

def scores_for_proteins(proteins: Iterable, genes_data: DataFrame, big_wig_path: str) -> Tuple[Dict, Namespace]:
    """Load conservation scores, average when needed, and transform into protein space."""

    bw = pyBigWig.open(big_wig_path)

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Function affected_motifs has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def affected_motifs(self, sites: Iterable[Site] = None):
        if self.were_affected_motifs_precomputed:
            return self.precomputed_affected_motifs

        from analyses.motifs import mutate_sequence

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File gene.py has 258 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from abc import ABC, abstractmethod
from collections import defaultdict

from Levenshtein import distance
from sqlalchemy import and_

Function switchGroupState has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function switchGroupState(group, state, time)
    {
        time = (time === undefined) ? 600 : time
        group.expanded = (state === undefined) ? !group.expanded : state

Function create_shapes has 53 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function create_shapes()
    {
        function radians(x){
            return x * Math.PI / 180
        }

Function ptm_variability_population_rare_substitutions has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

def ptm_variability_population_rare_substitutions(site_type, motif=None):
    """Compare variability of sequence in PTM sites
    with the variability of sequence outside of PTM sites,
    using frequency of rare substitutions.
    """

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Function proteins_and_genes has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

def proteins_and_genes(path='data/protein_data.tsv'):
    """Create proteins and genes based on data in a given file.

    If protein/gene already exists it will be skipped.

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Function create_app has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

def create_app(config_filename='config.py', config_override={}):
    """Factory function for flask application.

    Args:
        config_filename:

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Function create_ticker has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function create_ticker()
    {
        var site_nodes = nodes.filter(is_of_type(types.site));
        var drug_nodes = nodes.filter(is_of_type(types.drug));

Function node_dbl_click has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function node_dbl_click(node)
    {

        if(d3.event.defaultPrevented === false)
        {

Function init_edges has 48 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function init_edges(vis, edges)
    {
        links = vis.selectAll('.link')
            .data(edges)
            .enter().append('line')