def _clean_reads(kromsatel_args):
result_status = 1
try:
if kromsatel_args.kromsatel_mode == KromsatelModes.IlluminaPE:
runner = core.IlluminaPEKromsatelCore(kromsatel_args)
elif kromsatel_args.kromsatel_mode == KromsatelModes.Nanopore:
runner = core.LongReadKromsatelCore(kromsatel_args)
elif kromsatel_args.kromsatel_mode == KromsatelModes.IlluminaSE:
runner = core.IlluminaSEKromsatelCore(kromsatel_args)
# end if
runner.run()
except InvalidFastqError as err:
print_err(err.msg_to_print)
msg_to_log = '{}\n{}\n'.format(
err.msg_to_print,
err.msg_to_log_only
)
fs.log_to_file(msg_to_log, kromsatel_args.outdir_path)
except FatalError as err:
print_err(str(err))
else:
result_status = 0
# end try
return result_status
def main():
args = _parse_arguments()
_check_blastplus_dependencies(args)
print(str(args), end='\n\n')
db_fpath = _create_database(args)
args.set_database_path(db_fpath)
print('{} - Start.'.format(getwt()))
result_status = _clean_reads(args)
_cleanup(args)
if result_status == 0:
print('\n{} - Completed.'.format(getwt()))
print(' Output directory: `{}`'.format(args.outdir_path))
else:
print_err('\n\a{} - Completed with errors.'.format(getwt()))
# end if
return result_status
def _parse_arguments():
try:
args = src.parse_args.parse_args()
except FatalError as err:
print_err(str(err))
platformwise_exit(1)
# end try
return args
def _create_database(kromsatel_args):
try:
db_fpath = src.blast.create_reference_database(kromsatel_args)
except FatalError as err:
print_err(str(err))
platformwise_exit(1)
# end try
return db_fpath
def _check_blastplus_dependencies(kromsatel_args):
blastplus_dependencies = src.blast.get_blastplus_dependencies(kromsatel_args)
try:
for ncbi_program in blastplus_dependencies:
src.blast.check_program(ncbi_program)
# end for
except FatalError as err:
print_err(str(err))
platformwise_exit(1)
def log_to_file(message, outdir_path):
log_fpath = os.path.join(
outdir_path, 'error_log.log'
)
print_err('Logging to file `{}`'.format(log_fpath))
with open(log_fpath, 'wt') as log_file:
log_file.write('kromsatel start time: {}\n' \
.format(strftime('%Y-%m-%d %H:%M:%S', gmtime(START_TIME)))
)
log_file.write(message)
def _create_tmp_directory(self):
self.tmp_dir_path = os.path.join(
self.outdir_path, 'tmp'
)
try:
fs.create_dir(self.tmp_dir_path)
except FatalError as err:
print_err('\nError: cannot create temporary directory `{}`' \
.format(self.tmp_dir_path))
print_err(err)
print_err('The program will use the root of the output directory' \
' as a storage of temporary files')
self.tmp_dir_path = self.outdir_path
def try_rm_directory(dirpath):
try:
shutil.rmtree(dirpath)
except OSError as err:
print_err('\nWarning: cannot remove temporary directory `{}`'.format(dirpath))
print_err(str(err))
def rm_file_warn_on_error(file_path):
try:
os.unlink(file_path)
except OSError as oserr:
print_err('\nWarning: Cannot remove file `{}`'.format(file_path))
print_err( str(oserr) )