gen_bank_obj = Genbank_proteic_RAST(path_file_genBank)
taxo = gen_bank_obj.get_taxonomy_array()
print(gen_bank_obj.get_family())
print(file_name)
if len(taxo) == 7 or 'streptococcus_oralis' in file_name.lower():
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()) and len(taxo) == 7:
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())
if 'streptococcus_oralis' in file_name.lower():
family_obj = Family(designation='Streptococcaceae')
genus_obj = Genus(designation='Streptococcus')
specie_obj = Specie(designation='Streptococcus Oralis')
#name_bacterium_strain = file_name.split('-')[1]
#name_bacterium_strain = file_name.split('-')[0] + "-" + name_bacterium_strain.split('_')[2]
name_bacterium_strain = file_name
strain_obj = Strain(designation=name_bacterium_strain)
id_strain = strain_obj.get_id_strin_based_on_design_fk(6)
print(id_strain)
if id_strain == -1:
family_obj.create_family()
genus_obj.fk_family = family_obj.id_family
genus_obj.create_genus()
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())
print(genbank_file.get_strain())
print("--------")
##### Start test for one organisme
start_time = time.time()
print("Start organism")
for contig in listas:
print("pass contig: {0}".format(contig))
list_prot = xls_obj.get_proteins_ids_by_contig_id(contig)
for protein in list_prot:
protein_info = xls_obj.get_information_line_by_protein_id(protein)
print("End organism")