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

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""" Classes to generate random wc models

:Author: Mike Zheng <xzheng20@colby.edu>
:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-08-13

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

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    def run(self):
        """ Generate a :obj:`wc_lang` model

        Returns:
            :obj:`wc_lang.Model`: model

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)

        """

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

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"""
:Author: Ashwin Srinivasan <ashwins@mit.edu>
:Author: Bilal Shaikh <bilal.shaikh@columbia.edu>
:Date: 2018-06-06
:Copyright: 2018, Karr Lab

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

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Function gen_reactions has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

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    def gen_reactions(self, model, options):
        """ Generate reactions and rate laws of the random model

        Args:
            model (:obj:`wc_lang.Model`): model

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Function gen_genome has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

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

        # get options
        options = self.options

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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

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

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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

    """

Avoid deeply nested control flow statements.

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                        if five_prime_start < 0:
                            five_prime_start = 0
                        tu.genes.append(gene)

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                        if three_prime_end >= len(seq):
                            three_prime_end = len(seq) - 1
                        tu = self.knowledge_base.cell.loci.get_or_create(

Avoid deeply nested control flow statements.

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                        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(

Avoid deeply nested control flow statements.

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                        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)

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                        for k in range(operon_genes-1):

                            i_gene += 1

                            if i_gene >= len(chromosome.loci):

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                        if three_prime_end >= len(seq):
                            three_prime_end = len(seq) - 1
                        tu.end = three_prime_end

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                        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:]

Avoid deeply nested control flow statements.

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                        if five_prime_start < 0:
                            five_prime_start = 0
                        if three_prime_end >= len(seq):

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

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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')

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