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vanheeringen-lab/ANANSE

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ananse/peakpredictor.py

Summary

Maintainability
A
2 hrs
Test Coverage
C
74%

Function __init__ has a Cognitive Complexity of 18 (exceeds 15 allowed). Consider refactoring.
Open

    def __init__(
        self,
        reference=None,
        atac_bams=None,
        histone_bams=None,
Severity: Minor
Found in ananse/peakpredictor.py - About 45 mins 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 _load_cage has a Cognitive Complexity of 18 (exceeds 15 allowed). Consider refactoring.
Open

    def _load_cage(self, cage_tpms, regions=None, pfmscorefile=None, window=200):
        """Load CAGE data: Bidirectional regions and TPMs

        The CAGE file needs to contain two columns:
            1. regions in chr:start-end format
Severity: Minor
Found in ananse/peakpredictor.py - About 45 mins 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 _load_factor2motifs has a Cognitive Complexity of 17 (exceeds 15 allowed). Consider refactoring.
Open

    def _load_factor2motifs(self, pfmfile=None, indirect=True, factors=None):
        motifs = read_motifs(pfmfile, as_dict=True)
        f2m = {}

        valid_factors = []
Severity: Minor
Found in ananse/peakpredictor.py - About 35 mins 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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