family_obj = None
genus_obj = None
specie_obj = None
strain_obj = None
if '_phi' not in file_name.lower() or 'phage' not in file_name.lower():
family_obj = Family(designation=gen_bank_obj.get_family())
genus_obj = Genus(designation=gen_bank_obj.get_genus())
specie_obj = Specie(designation=gen_bank_obj.get_specie())
strain_obj = Strain(designation=gen_bank_obj.get_strain())
else:
family_obj = Family(designation='Phage no family')
genus_obj = Genus(designation='Phage no genuse')
specie_obj = Specie(designation='Phage no Specie')
strain_obj = Strain(
designation=gen_bank_obj.get_definition_of_the_organism())
family_obj.create_family()
genus_obj.fk_family = family_obj.id_family
genus_obj.create_genus()
specie_obj.fk_genus = genus_obj.id_genus
specie_obj.create_specie()
strain_obj.fk_specie = specie_obj.id_specie
strain_obj.create_strain()
#Test proteins from file
path_file_xls = cwd + '/RAST/SPREADSHEET/' + file_name
path_file_contig = cwd + '/RAST/CONTIGS/' + file_name[:-3] + 'contigs.fa'
xls_obj = Xls_gen_bank(path_file_xls)
############# TEST CONTIGS FASTA FILES ############# fasta_contigs_file = Fasta_contigs_RAST(cwd + '\RAST\\CONTIGS\\525717-Escherichia_coli_CFT079.contigs.fa') sequence_contig_nucleic = fasta_contigs_file.get_contig_seq_by_id(listas[0]) ############# TEST CONTIGS genbank FILES ############# genbank_file = Genbank_proteic_RAST(cwd + '\RAST\\GEN_BANK\\525717-Escherichia_coli_CFT079.gbk') aaaa = genbank_file.get_definition_of_the_organism() print(aaaa) www = genbank_file.get_taxonomy_array() print(www) print(type(genbank_file.data_gen_bank)) print(list(genbank_file.data_gen_bank.keys())[0]) qty_contig = genbank_file.get_number_of_contigs() print(genbank_file.get_family()) print(genbank_file.get_genus()) print(genbank_file.get_specie())