def _check_outdpath(self):
if self.argparse_args.outdir is None:
return
# end if
try:
fs.create_dir(self.argparse_args.outdir)
except FatalErrors as err:
error_msg = '\nError: cannot create directory `{}`:\n {}' \
.format(self.argparse_args.outdir, err)
raise FatalError(error_msg)
def _init_output(self):
fs.create_dir(self.outdir_path)
output_fpaths = (
self.major_outfpath,
self.minor_outfpath,
self.uncertain_outfpath,
)
for outfpath in output_fpaths:
fs.init_file(outfpath)
def _init_output(self):
fs.create_dir(self.outdir_path)
output_fpaths = (
self.frw_outfpath,
self.rvr_outfpath,
self.frw_unpaired_outfpath,
self.rvr_unpaired_outfpath,
)
for outfpath in output_fpaths:
fs.init_file(outfpath)
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 create_reference_database(kromsatel_args):
db_dirpath = os.path.join(kromsatel_args.outdir_path, 'blast_database')
fs.create_dir(db_dirpath)
db_fpath = os.path.join(db_dirpath, 'kromsatel_blast_database')
print('{} - Creating a reference database for BLAST:\n `{}`...'.format(
getwt(), db_fpath))
_make_blast_db(kromsatel_args.reference_fpath, db_fpath)
print('{} - Database: created'.format(getwt()))
if kromsatel_args.use_index:
print('{} - Indexing the database...'.format(getwt()))
_index_database(db_fpath)
print('{} - Index: created'.format(getwt()))
else:
print('Index will not be created for the database.')
# end if
return db_fpath
def _init_output(self):
fs.create_dir(self.outdir_path)
fs.init_file(self.outfpath)