Function gen_tus has a Cognitive Complexity of 52 (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) """

        options = self.options
        five_prime_len = options.get('five_prime_len') # 7 bp default (E. coli, wikipedia)

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Function gen_genome has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.

Open

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

        # get options
        options = self.options

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File genome.py has 372 lines of code (exceeds 250 allowed). Consider refactoring.

Open

"""
:Author: Ashwin Srinivasan <ashwins@mit.edu>
:Author: Bilal Shaikh <bilal.shaikh@columbia.edu>
:Author: Balazs Szigeti <balazs.szigeti@mssm.edu>
:Date: 2018-06-06

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
        options = self.options

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Function clean_and_validate_options has 65 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_components has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def gen_components(self):
        """ Takes random samples of the generated rnas and proteins and assigns them functions based on the included list of proteins and rnas"""

        cell = self.knowledge_base.cell
        cytosol = cell.compartments.get_one(id='c')

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Function gen_genome has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

        # get options
        options = self.options

Avoid deeply nested control flow statements.

Open

                        for gene in tu.genes:
                            # creates ProteinSpecipe object for corresponding protein sequence(s)
                            prot = self.knowledge_base.cell.species_types.get_or_create(
                                id='prot_{}'.format(gene.id),
                                __type=wc_kb.prokaryote.ProteinSpeciesType)

Avoid deeply nested control flow statements.

Open

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

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:

                            if genetic_code == 'normal':
                                codon_i = "".join(random.choice(BASES, p=PROB_BASES, size=(3,)))
                            elif genetic_code == 'reduced':

Avoid deeply nested control flow statements.

Open

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

Avoid deeply nested control flow statements.

Open

                        if three_prime_end >= len(seq):
                            three_prime_end = len(seq) - 1

Avoid deeply nested control flow statements.

Open

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

Avoid deeply nested control flow statements.

Open

                        for k in range(operon_genes-1):
                            i_gene += 1

                            if i_gene >= len(chromosome.loci):
                                break

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

Open

    def reduce_model(self):
        options = self.options
        genetic_code = options.get('genetic_code')
        seq_path = options.get('seq_path')

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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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