dict_values = {}
dict_values['287.5076'] = 'Pseudomonas_aeruginosa_4053 '
for file_name in list_files:
if file_name[:-4] in dict_values:
path_file_xls = cwd + '/RAST/Xls/' + file_name[:-3] + 'xls'
path_file_contig = cwd + '/RAST/CONTIG/' + file_name[:-3] + 'contigs.fa'
xls_file_exists = check_file_exits(path_file_xls)
contig_file_exist = check_file_exits(path_file_contig)
assert xls_file_exists == True and contig_file_exist == True, 'A file is missing'
xls_obj = Xls_gen_bank(path_file_xls, sheet_name = 'Sheet1')
contig_fasta_file_patric_obj = Fasta_contigs_RAST(path_file = path_file_contig)
qty_cntg = contig_fasta_file_patric_obj.get_qty_of_contigs()
list_cnt = contig_fasta_file_patric_obj.create_contigs_from_file()
gi_name = "Greg_" + dict_values[file_name[:-4]]
acc_value = "Greg_" + dict_values[file_name[:-4]]
person_responsible = 2
source_data = 3
phage_designation = dict_values[file_name[:-4]]
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)
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:
fasta_contig_obj = Fasta_contigs_RAST(path_file_contig)
qtity_cntg = fasta_contig_obj.get_qty_of_contigs()
list_cnt = fasta_contig_obj.create_contigs_from_file()
print("Hello")
#If not create a list with the contigs name
else:
list_cnt = []
list_contig_name = xls_obj.get_contigs_id_sorted()
for contig_element in list_contig_name:
contig_obj = Contig(head=contig_element, sequence='')
list_cnt.append(contig_obj)
#id_contig = -1, id_contig_db_outside = -1, head = "", sequence = " ", fk_id_whole_genome = -1
print(list_cnt)
list_of_proteins = xls_obj.create_proteins_from_file()
qty_proteins_loaded = len(list_of_proteins)
#Test get all proteins from a given contig id
list_prot = xls_obj.get_proteins_ids_by_contig_id("out_1")
print(type(list_prot))
print(list_prot[0])
#Test get information from a given protein id
www = xls_obj.get_information_line_by_protein_id(list_prot[0])
print(xls_obj.get_number_of_proteins())
print("end")
############# 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)