def test_from_kwargs():
"""Test NgdConfig initialises correctly from kwargs."""
config = NgdConfig.from_kwargs(parallel=2)
assert config.parallel == 2
with pytest.raises(ValueError):
NgdConfig.from_kwargs(garbage="wow")
def test_from_kwargs():
"""Test NgdConfig initialises correctly from kwargs."""
config = NgdConfig.from_kwargs(parallel=2)
assert config.parallel == 2
with pytest.raises(ValueError):
NgdConfig.from_kwargs(garbage="wow")
def NCBI_get_info_GenbankID(data_folder,
acc_ID,
debug,
assembly_level_given='complete'):
section_given = get_section(acc_ID, debug)
if debug:
debug_message("-----------------------------------------")
debug_message("NCBI_get_info_GenbankID function call", color="yellow")
## import module and class
import ncbi_genome_download
from ncbi_genome_download.config import NgdConfig
tries = ['bacteria', 'archaea']
for entry_tried in tries:
if debug:
debug_message("Trying with: " + entry_tried, color="yellow")
ngd_config = NgdConfig.from_kwargs(section=section_given,
file_formats='genbank',
assembly_accessions=acc_ID,
output=data_folder,
dry_run=True,
groups=entry_tried)
info = ncbi_genome_download.core.select_candidates(ngd_config)
if info:
if debug:
debug_message("It worked!", color="yellow")
return (entry_tried)
raise "**** ERROR: Something happen while connecting to NCBI... ***"
exit()
return (False)
def NCBI_get_info(section_given,
data_folder,
tax_ID_list,
debug,
assembly_level_given='complete',
group_given='bacteria'):
'''This function uses ncbi_genome_download to
create a dry run and return information of each entry provided
'''
## import module and class
import ncbi_genome_download
from ncbi_genome_download.config import NgdConfig
try:
ngd_config = NgdConfig.from_kwargs(
section=section_given,
file_formats='genbank',
taxids=tax_ID_list,
output=data_folder,
dry_run=True,
assembly_levels=assembly_level_given,
groups=group_given)
info = ncbi_genome_download.core.select_candidates(ngd_config)
except:
raise "**** ERROR: Something happen while connecting to NCBI... ***"
exit()
return (False)
####
if (len(info)) < 1:
print(
colored(
"No entries matched your filter. Please check the input options provided",
'yellow'))
exit()
## fill dictionary to simplify
dict_entries = {}
for entry, _ in info:
strain_name = ncbi_genome_download.core.get_strain(entry)
## debug messagess
if debug:
debug_message("", 'yellow')
print(entry)
string = entry['assembly_accession'] + '\t' + entry[
'organism_name'] + '\t' + strain_name
debug_message(string, 'yellow')
debug_message(
".....................................................................\n",
'yellow')
## fill dictionary
dict_entries[entry['assembly_accession']] = (entry['organism_name'],
strain_name)
## return
return (dict_entries)
