KarrLab/rand_wc_model_gen

View on GitHub

Showing 20 of 46 total issues

File core.py has 819 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Classes to generate random wc models

:Author: Mike Zheng <xzheng20@colby.edu>
:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-08-13
Severity: Major
Found in rand_wc_model_gen/model_gen/core.py - About 1 day to fix

    Function run has 268 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def run(self):
            """ Generate a :obj:`wc_lang` model
    
            Returns:
                :obj:`wc_lang.Model`: model
    Severity: Major
    Found in rand_wc_model_gen/model_gen/core.py - About 1 day to fix

      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_reactions has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
        Open

            def gen_reactions(self, model, options):
                """ Generate reactions and rate laws of the random model
        
                Args:
                    model (:obj:`wc_lang.Model`): model
        Severity: Minor
        Found in rand_wc_model_gen/model_gen/core.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 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

          Function gen_species has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
          Open

              def gen_species(self, model, options, misc_options):
                  """ Generate species type, species, and init concentrations of the random model
          
                  Args:
                      model (:obj:`wc_lang.Model`): model
          Severity: Minor
          Found in rand_wc_model_gen/model_gen/core.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 plot has 36 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

          def plot(model, results, filename):
              """ plot simulation results of the hard-coded rna model
          
              """
          
          
          Severity: Minor
          Found in rand_wc_model_gen/model_gen/core.py - About 1 hr 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

              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

                                          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

                                              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

                                                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

                                                  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

                            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

                            Function clean_and_validate_options has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                            Open

                                def clean_and_validate_options(self):
                                    """ Apply default options and validate options """
                                    options = self.options
                            
                                    id = options.get('id', 'rand_wc_model')
                            Severity: Minor
                            Found in rand_wc_model_gen/kb_gen/core.py - About 25 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

                            Severity
                            Category
                            Status
                            Source
                            Language