list_files = get_files_from_error_csv('error_files_list.csv')
#Uncomment this line for the first insertion
#list_files = get_list_ids_files_in_path('/RAST/SPREADSHEET/')
list_files = reversed(list_files)
list_files_error = []
list_files_done = []
print((list_files))
for file_name in list_files:
print(file_name)
#Load taxonomy
#try:
path_file_genBank = cwd + '/RAST/GEN_BANK/' + file_name[:-3] + 'gbk'
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 'staphylococcus_aureus' in file_name.lower():
#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)
value = check_file_exits(path_file_xls)
contig_file_exist = check_file_exits(path_file_contig)
#Test contigs from file
if contig_file_exist is True:
list_files = get_files_from_error_csv('error_files_list.csv')
#Uncomment this line for the first insertion
#list_files = get_list_ids_files_in_path('/RAST/SPREADSHEET/')
list_files = reversed(list_files)
list_files_error = []
list_files_done = []
print((list_files))
for file_name in list_files:
print(file_name)
#Load taxonomy
#try:
path_file_genBank = cwd + '/RAST/GEN_BANK/' + file_name[:-3] + 'gbk'
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')
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())
print(genbank_file.get_strain())
print("--------")
##### Start test for one organisme
start_time = time.time()
print("Start organism")
for contig in listas: