path_sequence + row[2])
print("Output {} done .".format(row[2]))
except IOError:
print("Error impossible to open {}".format(row[2]))
with open("impossible_opening.txt", "a") as nothing_open:
nothing_open.write(row[2] + "\n")
if __name__ == "__main__":
print("JGI ID to NCBI ID taxonomy !")
# Download the latest taxonomic database from the NCBI.
ncbi = NCBITaxa()
try:
version = ncbi._NCBITaxa__get_db_version()
print("version :", version)
except Exception:
version = None
# Get all parameters.
CSV_FILE, PATH_SEQUENCE = arguments()
print("csv :", CSV_FILE)
# Name of output csv.
output_csv = "output_fungi_csv.csv"
# Complete de csv file with ncbi taxonomic id.
add_ncbi_id_taxonym_in_csv(csv_file=CSV_FILE, output_csv_name=output_csv)
# Change the fasta file with the kraken instruction |kraken:taxon| and good ncbi id.
