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KarrLab/rand_wc_model_gen

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rand_wc_model_gen/kb_gen/genome.py

Summary

Maintainability
F
4 days
Test Coverage
F
8%

Function gen_tus has a Cognitive Complexity of 57 (exceeds 5 allowed). Consider refactoring.
Open

    def gen_tus(self):
        """ Creates transcription units with 5'/3' UTRs, polycistronic mRNAs, and other types of RNA (tRNA, rRNA, sRNA)

        """
Severity: Minor
Found in rand_wc_model_gen/kb_gen/genome.py - About 1 day 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

File genome.py has 303 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
:Author: Ashwin Srinivasan <ashwins@mit.edu>
:Author: Bilal Shaikh <bilal.shaikh@columbia.edu>
:Date: 2018-06-06
:Copyright: 2018, Karr Lab
Severity: Minor
Found in rand_wc_model_gen/kb_gen/genome.py - About 3 hrs to fix

    Function gen_rnas_proteins has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
    Open

        def gen_rnas_proteins(self):
        """ Creates RNA and protein objects corresponding to genes on chromosome

        """
        cell = self.knowledge_base.cell
    Severity: Minor
    Found in rand_wc_model_gen/kb_gen/genome.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 gen_genome has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

        def gen_genome(self):
        '''Construct knowledge base components and generate the DNA sequence'''

        # get options
        options = self.options
    Severity: Minor
    Found in rand_wc_model_gen/kb_gen/genome.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 clean_and_validate_options has 53 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def clean_and_validate_options(self):
        """ Apply default options and validate options """

        # Default options are loosely  based on Escherichia coli K-12
        # Nucleic Acids Research 41:D605-12 2013
    Severity: Major
    Found in rand_wc_model_gen/kb_gen/genome.py - About 2 hrs to fix

      Avoid deeply nested control flow statements.
      Open

                              if five_prime_start < 0:
                            five_prime_start = 0
                        tu.genes.append(gene)
      Severity: Major
      Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

        Avoid deeply nested control flow statements.
        Open

                                if three_prime_end >= len(seq):
                            three_prime_end = len(seq) - 1
                        tu = self.knowledge_base.cell.loci.get_or_create(
        Severity: Major
        Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

          Avoid deeply nested control flow statements.
          Open

                                  while operon_genes <= 1:
                            operon_genes = self.rand(operon_gen_num)[0]

                        # add 3', 5' UTRs to the ends of the transcription unit (upstream of first gene, downstream of last gene)
                        tu = self.knowledge_base.cell.loci.get_or_create(
          Severity: Major
          Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

            Avoid deeply nested control flow statements.
            Open

                                    for gene in tu.genes:
                            # creates ProteinSpecipe object for corresponding protein sequence(s)
                            # print(gene.get_seq()[0:3])
                            prot = cell.species_types.get_or_create(
                                id='prot_{}'.format(gene.id), __type=wc_kb.prokaryote.ProteinSpeciesType)
            Severity: Major
            Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

              Avoid deeply nested control flow statements.
              Open

                                      for k in range(operon_genes-1):

                            i_gene += 1

                            if i_gene >= len(chromosome.loci):
              Severity: Major
              Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

                Avoid deeply nested control flow statements.
                Open

                                        if three_prime_end >= len(seq):
                            three_prime_end = len(seq) - 1
                        tu.end = three_prime_end
                Severity: Major
                Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

                  Avoid deeply nested control flow statements.
                  Open

                                          while seq_str[i:i+3] in START_CODONS or seq_str[i:i+3] in STOP_CODONS:
                            # print('here')
                            codon_i = "".join(random.choice(
                                BASES, p=PROB_BASES, size=(3,)))
                            seq_str = seq_str[:i]+codon_i+seq_str[i+3:]
                  Severity: Major
                  Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

                    Avoid deeply nested control flow statements.
                    Open

                                            if five_prime_start < 0:
                            five_prime_start = 0
                        if three_prime_end >= len(seq):
                    Severity: Major
                    Found in rand_wc_model_gen/kb_gen/genome.py - About 45 mins to fix

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

                          def clean_and_validate_options(self):
        """ Apply default options and validate options """

        # Default options are loosely  based on Escherichia coli K-12
        # Nucleic Acids Research 41:D605-12 2013
                      Severity: Minor
                      Found in rand_wc_model_gen/kb_gen/genome.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

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

                                  gene_starts = numpy.int64(numpy.cumsum(numpy.concatenate(([0], gene_lens[0:-1])) +
                                                   numpy.concatenate((numpy.round(intergene_lens[0:1] / 2), intergene_lens[1:]))))
                      Severity: Major
                      Found in rand_wc_model_gen/kb_gen/genome.py and 1 other location - About 4 hrs to fix
                      rand_wc_model_gen/kb_gen/chrs_genes_tus.py on lines 91..92

                      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 77.

                      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 4 locations. Consider refactoring.
                      Open

                                          tu = self.knowledge_base.cell.loci.get_or_create(
                        id='tu_{}_{}'.format(i_chr + 1, i_gene + 1), __type=wc_kb.prokaryote.TranscriptionUnitLocus)
                      Severity: Major
                      Found in rand_wc_model_gen/kb_gen/genome.py and 3 other locations - About 1 hr to fix
                      rand_wc_model_gen/kb_gen/genome.py on lines 215..216
                      rand_wc_model_gen/kb_gen/genome.py on lines 355..356
                      rand_wc_model_gen/kb_gen/genome.py on lines 395..396

                      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 45.

                      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 4 locations. Consider refactoring.
                      Open

                                              tu = self.knowledge_base.cell.loci.get_or_create(
                            id='tu_{}_{}'.format(i_chr + 1, i_gene + 1), __type=wc_kb.prokaryote.TranscriptionUnitLocus)
                      Severity: Major
                      Found in rand_wc_model_gen/kb_gen/genome.py and 3 other locations - About 1 hr to fix
                      rand_wc_model_gen/kb_gen/genome.py on lines 215..216
                      rand_wc_model_gen/kb_gen/genome.py on lines 395..396
                      rand_wc_model_gen/kb_gen/genome.py on lines 406..407

                      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 45.

                      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 4 locations. Consider refactoring.
                      Open

                                      gene = self.knowledge_base.cell.loci.get_or_create(
                    id='gene_{}_{}'.format(i_chr + 1, i_gene + 1), __type=wc_kb.prokaryote.GeneLocus)
                      Severity: Major
                      Found in rand_wc_model_gen/kb_gen/genome.py and 3 other locations - About 1 hr to fix
                      rand_wc_model_gen/kb_gen/genome.py on lines 355..356
                      rand_wc_model_gen/kb_gen/genome.py on lines 395..396
                      rand_wc_model_gen/kb_gen/genome.py on lines 406..407

                      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 45.

                      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 4 locations. Consider refactoring.
                      Open

                                              tu = self.knowledge_base.cell.loci.get_or_create(
                            id='tu_{}_{}'.format(i_chr + 1, i_gene + 1), __type=wc_kb.prokaryote.TranscriptionUnitLocus)
                      Severity: Major
                      Found in rand_wc_model_gen/kb_gen/genome.py and 3 other locations - About 1 hr to fix
                      rand_wc_model_gen/kb_gen/genome.py on lines 215..216
                      rand_wc_model_gen/kb_gen/genome.py on lines 355..356
                      rand_wc_model_gen/kb_gen/genome.py on lines 406..407

                      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 45.

                      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

                              PROB_BASES = [(1 - mean_gc_frac) / 2, mean_gc_frac /
                      2, mean_gc_frac/2, (1-mean_gc_frac)/2]
                      Severity: Major
                      Found in rand_wc_model_gen/kb_gen/genome.py and 1 other location - About 1 hr to fix
                      rand_wc_model_gen/kb_gen/chrs_genes_tus.py on lines 81..82

                      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 43.

                      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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