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BjornFJohansson/pydna

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src/pydna/dseq.py

Summary

Maintainability
F
1 wk
Test Coverage

File dseq.py has 1427 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
# This code is part of the Python-dna distribution and governed by its
Severity: Major
Found in src/pydna/dseq.py - About 3 days to fix

    Dseq has 47 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class Dseq(_Seq):
    """Dseq holds information for a double stranded DNA fragment.

    Dseq also holds information describing the topology of
    the DNA fragment (linear or circular).
    Severity: Minor
    Found in src/pydna/dseq.py - About 6 hrs to fix

      Function __init__ has a Cognitive Complexity of 39 (exceeds 5 allowed). Consider refactoring.
      Open

          def __init__(
        self,
        watson,
        crick=None,
        ovhg=None,
      Severity: Minor
      Found in src/pydna/dseq.py - About 5 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 __repr__ has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
      Open

          def __repr__(self):
        """Returns a representation of the sequence, truncated if
        longer than 30 bp"""

        if len(self) > Dseq.trunc:
      Severity: Minor
      Found in src/pydna/dseq.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

      Function cutsite_is_valid has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
      Open

          def cutsite_is_valid(self, cutsite):
        """Returns False if:
        - Cut positions fall outside the sequence (could be moved to Biopython)
        - Overhang is not double stranded
        - Recognition site is not double stranded or is outside the sequence
      Severity: Minor
      Found in src/pydna/dseq.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 T4 has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
      Open

          def T4(self, nucleotides=None):
        """Fill in five prime protruding ends and chewing back
        three prime protruding ends by a DNA polymerase providing both
        5'-3' DNA polymerase activity and 3'-5' nuclease acitivty
        (such as T4 DNA polymerase). This can be done in presence of any
      Severity: Minor
      Found in src/pydna/dseq.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 __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
      Open

          def __getitem__(self, sl):
        """Returns a subsequence. This method is used by the slice notation"""

        if not self.circular:
            x = len(self.crick) - self.ovhg - len(self.watson)
      Severity: Minor
      Found in src/pydna/dseq.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

      Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(
      Severity: Minor
      Found in src/pydna/dseq.py - About 45 mins to fix

        Function quick has 5 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def quick(
        Severity: Minor
        Found in src/pydna/dseq.py - About 35 mins to fix

          Function from_string has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def from_string(
          Severity: Minor
          Found in src/pydna/dseq.py - About 35 mins to fix

            Function translate has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def translate(self, table="Standard", stop_symbol="*", to_stop=False, cds=False, gap="-"):
            Severity: Minor
            Found in src/pydna/dseq.py - About 35 mins to fix

              Function _fill_in_five_prime has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                  def _fill_in_five_prime(self, nucleotides):
        stuffer = ""
        type, se = self.five_prime_end()
        if type == "5'":
            for n in _rc(se):
              Severity: Minor
              Found in src/pydna/dseq.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

              Function __add__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                  def __add__(self, other):
        """Simulates ligation between two DNA fragments.

        Add other Dseq object at the end of the sequence.
        Type error is raised if any of the points below are fulfilled:
              Severity: Minor
              Found in src/pydna/dseq.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

              Function _fill_in_three_prime has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                  def _fill_in_three_prime(self, nucleotides):
        stuffer = ""
        type, se = self.three_prime_end()
        if type == "5'":
            for n in _rc(se):
              Severity: Minor
              Found in src/pydna/dseq.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

              Avoid too many return statements within this function.
              Open

                      return True
              Severity: Major
              Found in src/pydna/dseq.py - About 30 mins to fix

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