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vanheeringen-lab/gimmemotifs

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gimmemotifs/tools/memew.py

Summary

Maintainability
B
4 hrs
Test Coverage
A
96%

Function parse has a Cognitive Complexity of 34 (exceeds 15 allowed). Consider refactoring.
Open

    def parse(self, fo):
        """
        Convert MEME output to motifs

        Parameters
Severity: Minor
Found in gimmemotifs/tools/memew.py - About 3 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

Avoid deeply nested control flow statements.
Open

                        if not pfm:
                            pfm = [[0 for x in range(4)] for x in range(len(match))]
                        for pos in range(len(match)):
Severity: Major
Found in gimmemotifs/tools/memew.py - About 45 mins to fix

    Avoid deeply nested control flow statements.
    Open

                            for pos in range(len(match)):
                            if match[pos] in nucs:
                                pfm[pos][nucs[match[pos]]] += 1
                            else:
                                for i in range(4):
    Severity: Major
    Found in gimmemotifs/tools/memew.py - About 45 mins to fix

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