Function build_obs_peptide has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def build_obs_peptide(self, data, i, description):
        """Build observation objects from obj.
        Go into observations collection.
        Args:
            data (:obj:`Obj`): source object.

• Read up
  Read up

Avoid deeply nested control flow statements.

Open

                        if seqs:
                            subunit.sequence = next((seq['Sequence'] for seq in seqs if seq['Entry'] == xref.id), seqs[0]['Sequence'])
                            iupac_seq = re.sub(r'[^' + Bio.Alphabet.IUPAC.IUPACProtein.letters + r']', '', subunit.sequence)
                            subunit.molecular_weight = \
                                + Bio.SeqUtils.molecular_weight(iupac_seq, seq_type='protein') \

Function load_content has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def load_content(self):
        '''Load kegg_reactions into MongoDB
        '''
        _, _, collection = self.con_db(self.collection)

• Read up
  Read up

Avoid deeply nested control flow statements.

Open

                        if doc is not None:
                            uniprot_id.append(doc)
            yield {'org_gene': org_gene_str,

Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self,

Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self, MongoDB, db, collection, username, password,

Function filter_comments has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def filter_comments(self, comments, enz_id):
        filtered_comments = []
        for comment in comments:
            has_comment = False
            for enz_ref_id in comment['enz_ref_ids']:

• Read up
  Read up

Function fill_ec_meta has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def fill_ec_meta(self, start=0):
        """Fill sabio documents with ec meta information.
        """
        query = {}
        docs = self.collection.find(filter=query)

• Read up
  Read up

Avoid deeply nested control flow statements.

Open

                        if "YMDB" in loc["reference"]:
                            values_y.append({"type": "cellular_location",
                                            "value": l})
                        else:
                            values_e.append({"type": "cellular_location",

Avoid deeply nested control flow statements.

Open

                        if re.search(pattern, k):
                            value["value"] = v * 3600.0
                            genotype["cellLine"] = k
                            value["units"] = "s"
                        elif k == "note":

Avoid deeply nested control flow statements.

Open

                        if rel_dirname == '.':
                            rel_subdirname = subdirname
                        else:
                            rel_subdirname = os.path.join(rel_dirname, subdirname)
                        os.makedirs(os.path.join(root_tmp_path, rel_subdirname))

Avoid deeply nested control flow statements.

Open

                        if isinstance(val, str):
                            entity["identifiers"].append({"namespace": key,
                                                        "value": val})
                        elif isinstance(val, list):
                            for _id in val:

Avoid deeply nested control flow statements.

Open

                        for ref in val:
                            source.append({"namespace": list(ref.keys())[0],
                                        "value": list(ref.values())[0]})
                    elif key == "gene_name":

Avoid deeply nested control flow statements.

Open

                        if rel_dirname == '.':
                            rel_filename = filename
                        else:
                            rel_filename = os.path.join(rel_dirname, filename)
                        os.symlink(os.path.join(root_cache_path, rel_filename),

Consider simplifying this complex logical expression.

Open

                    if other_part.specie.structure == part.specie.structure and \
                            other_part.specie.id == part.specie.id and \
                            ((other_part.compartment is None and part.compartment is None) or
                                other_part.compartment.id == part.compartment.id) and \
                            numpy.sign(other_part.coefficient) == numpy.sign(part.coefficient):

Function fill_trna_primary has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def fill_trna_primary(self, file_location, sheet_name='tRNA', start_row=[0],

Function fill_trna_collection has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def fill_trna_collection(self, file_location, start_row=0,

Function create_kinetic_law_from_sbml has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def create_kinetic_law_from_sbml(self, id, sbml, specie_properties, functions, units):

Function _flatten_conc_obj has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def _flatten_conc_obj(self, obj, ncbi_id, species_name, _id, source='ECMDB'):

Function run has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(self, in_obo_filename=None, in_tsv_filename=None, in_monomers_filename=None, max_num_proteins=None,