Read a lstinfo file containing the list of genomes with information (L90, genome size etc.).
1 line per genome, 4 or 5 columns:
[gembase_name] orig_name gsize nb_conts L90
1 line per genome, 4 required columns (Others will just be ignored):
to_annotate gsize nb_conts L90
Check that the given genome file exists in dbpath. Otherwise, put an error message,
and ignore this file.
Check that the given genome file (to_annotate column) exists in dbpath. If not, check if it is in tmp_path. If in none of those 2 folders, put a warning message and ignore this file.
# If invalid values, warnng message and ignore genome
exceptValueError:
logger.warning("For genome {}, at least one of your columns 'gsize', 'nb_conts' or 'L90' contains a non numeric character. This genome will be ignored.".format(gname))
continue
# Check if genome file exists
ifnotos.path.isfile(gpath):
logger.warning(("{} genome file does not exist in the given database. "
"It will be ignored.".format(gpath)))
continue
# If it does not exist, look at it in tmp_file (can come from a concatenation
# of several files in db_path)
gpath=os.path.join(tmp_path,gname)
# If still not in tmp_dir, warning message and ignore genome
ifnotos.path.isfile(gpath):
logger.warning(("{} genome file does not exist in the given "