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Function compute_intermediate_sequences has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def compute_intermediate_sequences(self):
        """
        Given the step in the protocol, computes the intermediate mutated
        coding sequences.
Severity: Minor
Found in FluGibson/nucleotide_converter.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

Similar blocks of code found in 3 locations. Consider refactoring.
Open

            codon1 = self.src.seq[(i * 3):(i * 3 + 3)]
Severity: Major
Found in FluGibson/nucleotide_converter.py and 2 other locations - About 45 mins to fix
FluGibson/nucleotide_converter.py on lines 95..95
FluGibson/nucleotide_protein_converter.py on lines 74..74

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 35.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Avoid deeply nested control flow statements.
Open

                for drxn in ['fw', 're']:
                    primer_data['part'] = n
                    primer_data['{0}_cloning_primer'.format(drxn)] =\
                        str(d['{0}_cloning_primer'.format(drxn)].seq)
                master_cloning_primers.append(primer_data)
Severity: Major
Found in examples/seal_h3n8/compute_primers.py - About 45 mins to fix

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

                codon2 = self.des.seq[(i * 3):(i * 3 + 3)]
    Severity: Major
    Found in FluGibson/nucleotide_converter.py and 2 other locations - About 45 mins to fix
    FluGibson/nucleotide_converter.py on lines 94..94
    FluGibson/nucleotide_protein_converter.py on lines 74..74

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 35.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Avoid deeply nested control flow statements.
    Open

                    if k in f:
                    segment = v
            backbone = plasmids['pDZ-{0}-split2'.format(segment)]
    Severity: Major
    Found in examples/seal_h3n8/compute_primers.py - About 45 mins to fix

      Similar blocks of code found in 3 locations. Consider refactoring.
      Open

                  codon = self.src_nt.seq[codon_pos*3:codon_pos*3 + 3]
      Severity: Major
      Found in FluGibson/nucleotide_protein_converter.py and 2 other locations - About 45 mins to fix
      FluGibson/nucleotide_converter.py on lines 94..94
      FluGibson/nucleotide_converter.py on lines 95..95

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 35.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

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

          def get_part(self, part_name):
        """
        Returns the SeqRecord object whose id is the part_name.

        Paramters:
      Severity: Minor
      Found in FluGibson/primer_designer.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 compute_assembly_steps has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
      Open

          def compute_assembly_steps(self):
        """
        Computes the mutation assembly steps based on the distance graph.

        The algorithm is as such:
      Severity: Minor
      Found in FluGibson/nucleotide_converter.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 compute_pcr_fragments has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
      Open

          def compute_pcr_fragments(self):
        """
        Computes the PCR fragments to assemble, based on the protocol. The
        protocol currently specifies the codon positions to be mutated. For
        example, if we have:
      Severity: Minor
      Found in FluGibson/nucleotide_converter.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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