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reimandlab/Visualistion-Framework-for-Genome-Mutations

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website/analyses/conservation/scores.py

Summary

Maintainability
A
3 hrs
Test Coverage

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)
Severity: Minor
Found in website/analyses/conservation/scores.py - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function extract_track has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def extract_track(protein_data: DataFrame, protein, chrom: str, bw) -> List[float]:
    """Extract scores from given BigWig file for coding region of given protein.

    Scores for each nucleotide in the CDS will be returned,
    and the length of the track will be verified against
Severity: Minor
Found in website/analyses/conservation/scores.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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