def load_toxoplasma_mutant(raw_data, row): # move down to attribute count row += 1 attribute_count = int(raw_data[row][1]) toxoplasma_mutant_list = [] if attribute_count > 0: row += 1 for i in range(0, attribute_count): # move down to data row += 1 name = raw_data[row][0] name = name[1:-1] target_name = raw_data[row][1] target_name = target_name[1:-1] background = raw_data[row][2] background = background[1:-1] selection = raw_data[row][3] selection = selection[1:-1] mutation_type = raw_data[row][4] mutation_type = mutation_type[1:-1] promoter = raw_data[row][5] promoter = promoter[1:-1] organism = raw_data[row][6] organism = organism[1:-1] target_gene = raw_data[row][7] target_gene = target_gene[1:-1] # load organism organism = importer_organism.get_organism(organism) # load ontology term background = importer_ontology.get_ontology_term( "toxoplasma mutant", "toxoplasma mutant background", background ) # get ontology term selection = importer_ontology.get_ontology_term( "toxoplasma mutant", "toxoplasma mutant selection", selection ) # get ontology term mutation_type = importer_ontology.get_ontology_term( "toxoplasma mutant", "toxoplasma mutant mutation type", mutation_type ) # get ontology term promoter = importer_ontology.get_ontology_term( "toxoplasma mutant", "toxoplasma mutant promoter", promoter ) # get ontology term # load of Genes if target_gene: target_gene = importer_gene.get_gene(target_gene) if ( name and target_name and background and selection and mutation_type and promoter and organism and target_gene ): toxoplasma_mutant = importer_toxoplasma_mutant.get_toxoplasma_mutant_with_target_gene( name, target_name, background, selection, mutation_type, promoter, organism, target_gene ) # return toxoplasma mutant toxoplasma_mutant_list.append(toxoplasma_mutant) elif name and target_name and background and selection and mutation_type and promoter and organism: toxoplasma_mutant = importer_toxoplasma_mutant.get_toxoplasma_mutant_without_target_gene( name, target_name, background, selection, mutation_type, promoter, organism ) # return toxoplasma mutant toxoplasma_mutant_list.append(toxoplasma_mutant) return toxoplasma_mutant_list
def load_antibody(raw_data, row): # move down to attribute count row += 1 attribute_count = int(raw_data[row][1]) antibody_list = [] if attribute_count > 0: row += 1 for i in range(0, attribute_count): # move down to data row += 1 name = raw_data[row][0] name = name[1:-1] target_name = raw_data[row][1] target_name = target_name[1:-1] tagged = raw_data[row][2] tagged = tagged[1:-1] tag_target = raw_data[row][3] tag_target = tag_target[1:-1] source = raw_data[row][4] source = source[1:-1] catalog_number = raw_data[row][5] catalog_number = catalog_number[1:-1] epitope = raw_data[row][6] epitope = epitope[1:-1] lot_number = raw_data[row][7] lot_number = lot_number[1:-1] ifa_localization = raw_data[row][8] ifa_localization = ifa_localization[1:-1] chip_peaks = raw_data[row][9] chip_peaks = chip_peaks[1:-1] monoclonal = raw_data[row][10] monoclonal = monoclonal[1:-1] isotype = raw_data[row][11] isotype = isotype[1:-1] immunogen_source = raw_data[row][12] immunogen_source = immunogen_source[1:-1] conjugation = raw_data[row][13] conjugation = conjugation[1:-1] validated = raw_data[row][14] validated = validated[1:-1] url = raw_data[row][15] url = url[1:-1] animal_host = raw_data[row][16] animal_host = animal_host[1:-1] target_gene = raw_data[row][17] target_gene = target_gene[1:-1] # load ontology term animal_host = importer_ontology.get_ontology_term( "antibody", "antibody host organism", animal_host ) # get ontology term # load of Genes if target_gene: target_gene = importer_gene.get_gene(target_gene) if name and target_name and target_gene: antibody = importer_antibody.get_antibody_with_target_gene( name, target_name, tagged, tag_target, source, catalog_number, epitope, lot_number, ifa_localization, chip_peaks, monoclonal, isotype, immunogen_source, conjugation, validated, url, animal_host, target_gene, ) # return antibody antibody_list.append(antibody) elif name and target_name: antibody = importer_antibody.get_antibody_without_target_gene( name, target_name, tagged, tag_target, source, catalog_number, epitope, lot_number, ifa_localization, chip_peaks, monoclonal, isotype, immunogen_source, conjugation, validated, url, animal_host, ) # return antibody antibody_list.append(antibody) return antibody_list