def build_menu_toa_go():
'''
Build the menu Gene Ontology.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_go_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Download functional annotations from Gene Ontology server')
print(f' 2. Load data into {xlib.get_toa_name()} database')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_manage_genomic_database(xlib.get_toa_type_download_data(), xlib.get_toa_data_go_code())
elif option == '2':
ctoa.form_manage_genomic_database(xlib.get_toa_type_load_data(), xlib.get_toa_data_go_code())
elif option == 'X':
break
def build_menu_toa_basic_data():
'''
Build the menu Basic data.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_basic_data_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Recreate genomic dataset file')
print( ' 2. Edit genomic file')
print()
print( ' 3. Recreate species file')
print( ' 4. Edit species file')
print()
print( ' 5. Download other basic data')
print()
print(f' 6. Load data into {xlib.get_toa_name()} database')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
cbioinfoapp.form_recreate_data_file(xtoa.get_dataset_file())
elif option == '2':
cbioinfoapp.form_edit_data_file(xtoa.get_dataset_file())
elif option == '3':
cbioinfoapp.form_recreate_data_file(xtoa.get_species_file())
elif option == '4':
cbioinfoapp.form_edit_data_file(xtoa.get_species_file())
elif option == '5':
ctoa.form_manage_genomic_database(xlib.get_toa_type_download_data(), xlib.get_toa_data_basic_data_code())
elif option == '6':
ctoa.form_manage_genomic_database(xlib.get_toa_type_load_data(), xlib.get_toa_data_basic_data_code())
elif option == 'X':
break
def form_manage_genomic_database(process_type, genomic_database):
'''
Manage processes of genomic database.
'''
# initialize the control variable
OK = True
# set the genomica database name
if genomic_database == xlib.get_toa_data_basic_data_code():
name = xlib.get_toa_data_basic_data_name()
elif genomic_database == xlib.get_toa_data_gymno_01_code():
name = xlib.get_toa_data_gymno_01_name()
elif genomic_database == xlib.get_toa_data_dicots_04_code():
name = xlib.get_toa_data_dicots_04_name()
elif genomic_database == xlib.get_toa_data_monocots_04_code():
name = xlib.get_toa_data_monocots_04_name()
elif genomic_database == xlib.get_toa_data_refseq_plant_code():
name = xlib.get_toa_data_refseq_plant_name()
elif genomic_database == xlib.get_toa_data_taxonomy_code():
name = xlib.get_toa_data_taxonomy_name()
elif genomic_database == xlib.get_toa_data_nt_code():
name = xlib.get_toa_data_nt_name()
elif genomic_database == xlib.get_toa_data_viridiplantae_nucleotide_gi_code(
):
name = xlib.get_toa_data_viridiplantae_nucleotide_gi_name()
elif genomic_database == xlib.get_toa_data_nr_code():
name = xlib.get_toa_data_nr_name()
elif genomic_database == xlib.get_toa_data_viridiplantae_protein_gi_code():
name = xlib.get_toa_data_viridiplantae_protein_gi_name()
elif genomic_database == xlib.get_toa_data_gene_code():
name = xlib.get_toa_data_gene_name()
elif genomic_database == xlib.get_toa_data_interpro_code():
name = xlib.get_toa_data_interpro_name()
elif genomic_database == xlib.get_toa_data_go_code():
name = xlib.get_toa_data_go_name()
# print the header
clib.clear_screen()
if process_type == xlib.get_toa_type_build_blastplus_db():
clib.print_headers_with_environment(f'Build {name} for BLAST+')
elif process_type == xlib.get_toa_type_build_diamond_db():
clib.print_headers_with_environment(f'Build {name} for DIAMOND')
elif process_type == xlib.get_toa_type_build_gilist():
clib.print_headers_with_environment(f'Build {name}')
elif process_type == xlib.get_toa_type_build_proteome():
clib.print_headers_with_environment(f'Build {name} proteome')
elif process_type == xlib.get_toa_type_download_data():
clib.print_headers_with_environment(
f'Download {name} functional annotations')
elif process_type == xlib.get_toa_type_load_data():
clib.print_headers_with_environment(
f'Load {name} data in {xlib.get_toa_name()} database')
print(xlib.get_separator())
# confirm the process run
if OK:
OK = clib.confirm_action(f'The {name} process is going to be run.')
# run the process
if OK:
devstdout = xlib.DevStdOut(xtoa.manage_genomic_database.__name__)
OK = xtoa.manage_genomic_database(process_type,
genomic_database,
devstdout,
function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')