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examples/modomics_analysis.py

Summary

Maintainability
B
6 hrs
Test Coverage

Avoid deeply nested control flow statements.
Open

                if monomer not in monomer_freq:
                    monomer_freq[monomer] = 0
                monomer_freq[monomer] += copies
Severity: Major
Found in examples/modomics_analysis.py - About 45 mins to fix

    Avoid deeply nested control flow statements.
    Open

                    if can_code not in can_monomer_freq:
                    can_monomer_freq[can_code] = 0
                can_monomer_freq[can_code] += copies
    Severity: Major
    Found in examples/modomics_analysis.py - About 45 mins to fix

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

      fig.savefig(os.path.join('examples', 'modomics.trna.analysis.pdf'),
            transparent=True,
            bbox_inches=matplotlib.transforms.Bbox([[0.45, -0.31], [5.86, 1.35]]))
      Severity: Major
      Found in examples/modomics_analysis.py and 1 other location - About 1 hr to fix
      examples/modomics_analysis.py on lines 82..84

      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 42.

      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

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

      fig.savefig(os.path.join('examples', 'modomics.trna.analysis.svg'),
            transparent=True,
            bbox_inches=matplotlib.transforms.Bbox([[0.45, -0.31], [5.86, 1.35]]))
      Severity: Major
      Found in examples/modomics_analysis.py and 1 other location - About 1 hr to fix
      examples/modomics_analysis.py on lines 85..87

      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 42.

      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

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

      for code in monomer_freq.keys():
    monomer_freq[code] *= (1. + doubling_time / half_life)
      Severity: Minor
      Found in examples/modomics_analysis.py and 1 other location - About 45 mins to fix
      examples/modomics_analysis.py on lines 46..47

      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

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

      for monomer in can_monomer_freq.keys():
    can_monomer_freq[monomer] *= (1. + doubling_time / half_life)
      Severity: Minor
      Found in examples/modomics_analysis.py and 1 other location - About 45 mins to fix
      examples/modomics_analysis.py on lines 44..45

      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

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

      canonical_monomers = [
    bpforms.rna_alphabet.monomers.A,
    bpforms.rna_alphabet.monomers.C,
    bpforms.rna_alphabet.monomers.G,
    bpforms.rna_alphabet.monomers.U,
      Severity: Minor
      Found in examples/modomics_analysis.py and 1 other location - About 40 mins to fix
      examples/homo_sapiens_rna/curate.py on lines 21..24

      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 34.

      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

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