# setup stuff: check for command line args, etc.
if __name__ == '__main__':
# check if database name(s) passed on command line
if len(sys.argv) > 1:
fasta_files = sys.argv[1:]
# if not, browse to database file
else:
database = r'C:\Xcalibur\database' # set a default to speed up browsing
if not os.path.exists(database):
database = os.getcwd()
fasta_files = fasta_lib.get_files(database,
[('FASTA files', '*.fasta'),
('Zipped FASTA files', '*.gz'),
('All files', '*.*')],
'Select a FASTA database')
if not fasta_files: sys.exit() # cancel button repsonse
# print version info, etc. (here because of the loop)
print('===============================================================')
print(' count_fasta.py, v 1.1.0, written by Phil Wilmarth, OHSU, 2017 ')
print('===============================================================')
# call counter function for each fasta file
print('start', time.ctime())
for fasta_file in fasta_files:
try:
fasta_counter(fasta_file)
except FileNotFoundError: # FastaReader class raises exception if file not found
return
# print program name and version
print('==========================================================')
print(' program check_fasta.py, v1.0.0, Phil Wilmarth, OHSU 2020 ')
print('==========================================================')
# browse to the database
database = r"C:\Xcalibur\database"
if not os.path.exists(database):
database = os.getcwd()
file_ext_list = [('FASTA files', '*.fasta'), ('FASTA files', '*.fa'),
('FASTA files', '*.gz')]
fasta_files = fasta_lib.get_files(database, file_ext_list, 'Select a FASTA database')
if not fasta_files:
sys.exit() # cancel button repsonse
# create a log file to mirror screen output
_folder = os.path.split(fasta_files[0])[0]
log_obj = open(os.path.join(_folder, 'fasta_utilities.log'), 'a')
write = [None, log_obj]
fasta_lib.time_stamp_logfile('\n>>> starting: check_fasta.py', log_obj)
# process the FASTA files
for fasta_file in fasta_files:
try:
fasta_checker(fasta_file, write)
except FileNotFoundError:
pass
