diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py
index bb8d5f98b55383cc7b37cb9959cb224fc794965a..1f91485ca7742d5998e37c45e588ee53e137b58d 100644
--- a/PanACoTA/subcommands/prepare.py
+++ b/PanACoTA/subcommands/prepare.py
@@ -190,15 +190,15 @@ def main(cmd, NCBI_species, NCBI_taxid, outdir, tmp_dir, threads, no_refseq, onl
# Do only mash filter. Genomes must be already downloaded, and there must be a file with
# all information on these genomes (L90 etc.)
else:
+ logger.warning('You asked to run only mash steps.')
if not os.path.exists(info_file): # info-file missing -> error and exit
logger.error(f"Your info file {info_file} does not exist. Please Provide the "
"right name/path, or remove the '--mash-only option to rerun "
"quality control.")
sys.exit(1)
- logger.info(("You want to rerun only mash steps. Getting information "
+ logger.info(("You want to run only mash steps. Getting information "
"from {}").format(info_file))
genomes = utils.read_genomes_info(info_file, species_linked, )
-
# Run Mash
# genomes : {genome_file: [genome_name, orig_name, path_to_seq_to_annotate, size,
# nbcont, l90]}
@@ -354,7 +354,7 @@ def check_args(parser, args):
# If user wants only mash steps, check that he gave info file
if args.only_mash and not args.from_info:
parser.error("If you want to run only Mash filtering steps, please give the "
- "info file with the required information (see '--info' option")
+ "info file with the required information (see '--info' option)")
# WARNINGS
# User did not specify a species name
@@ -375,11 +375,11 @@ def check_args(parser, args):
# Warn if user gave info file, but does not ask to run only Mash -> info file will be ignored
if args.from_info and not args.only_mash:
- message = ("You gave an info file (--info option), but did not ask to run only Mash "
+ message = (" !! You gave an info file (--info option), but did not ask to run only Mash "
"step (-M option). Your info file will be ignored (and renamed with '.back' "
"at the end), and another one will "
"be created with the new calculated values.")
- print(colored(message))
+ print(colored(message, "yellow"))
return args
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index 129a83b8b332690cf01691f283e4113506d81d4b..c03408a0d8b6f38f6da97b02d8da252a5f7d1528 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -620,7 +620,7 @@ def read_genomes(list_file, name, date, dbpath, tmp_path):
dict
{genome: spegenus.date} spegenus.date = name.date
"""
- logger = logging.getLogger("utils")
+ logger = logging.getLogger("prepare.utils")
logger.info("Reading genomes")
genomes = {}
# Check that given list file exists
@@ -686,15 +686,13 @@ def read_genomes(list_file, name, date, dbpath, tmp_path):
return genomes
-def read_genomes_info(list_file, name, date, dbpath, dbpath2):
+def read_genomes_info(list_file, name, date=None, logger=None):
"""
Read a lstinfo file containing the list of genomes with information (L90, genome size etc.).
1 line per genome, 4 required columns (Others will just be ignored):
to_annotate gsize nb_conts L90
- Check that the given genome file (to_annotate column) exists in dbpath or in dbpath2
- (files can be split into 2 different folders). If in none of those 2 folders, put a
- warning message and ignore this file.
+ Check that the given genome file (to_annotate column) exists.
Parameters
----------
@@ -704,13 +702,9 @@ def read_genomes_info(list_file, name, date, dbpath, dbpath2):
Default species name
date : str
Default date
- dbpath : str
- path to folder containing genome files to annotate
- dbpath2 : str
- path to other folder which can contain the genome files to annotate. For example,
- if it comes from a previous run of 'PanACoTA annotate' where sequences needed to be
- modified to be ready for annotation (for example, merging several contig files in one
- file, split at each stretch of 5 'N', etc.).
+ logger : logging.Logger
+ logger object to write log information
+
Returns
-------
@@ -719,17 +713,21 @@ def read_genomes_info(list_file, name, date, dbpath, dbpath2):
[spegenus.date, path_orig_seq, path_to_splitSequence, size, nbcont, l90]
}
"""
- logger = logging.getLogger("utils")
+ if not logger:
+ logger = logging.getLogger("prepare.utils")
logger.info(f"Reading given information on your genomes in {list_file}")
genomes = {}
- spegenus = "{}.{}".format(name, date)
+ if name and date:
+ spegenus = "{}.{}".format(name, date)
column_order = {} # Put the number of column corresponding to each field
if not os.path.isfile(list_file):
- logger.error(("ERROR: You used the '--info <filename>' option, meaning that <filename> "
- "contains information on each sequence provided (L90, nb contigs etc.). "
- "However, the provided genome information file '{}' does not exist. "
- "Please provide a listinfo file.\n Ending program.").format(list_file))
+ logger.error(f"ERROR: The info file {list_file} that you gave does not exist. "
+ "Please provide the right path/name for this file.\nEnding program.")
sys.exit(1)
+ message_no_header = (f"ERROR: It seems that your info file {list_file} does not have a "
+ "header, or this header does not have, at least, the required "
+ "columns tab separated: to_annotate, gsize nb_conts and L90 (in any "
+ "order).\nEnding program.")
with open(list_file, "r") as lff:
for line in lff:
line = line.strip()
@@ -740,16 +738,12 @@ def read_genomes_info(list_file, name, date, dbpath, dbpath2):
found = [head for head in ["to_annotate", "gsize", "nb_conts", "L90"]
if head in column_order]
if len(found) != 4:
- logger.error("ERROR: Your information file does not have the required "
- "columns, tab separated: to_annotate, gsize, nb_conts and L90 "
- "(in any order) \n Ending program.")
+ logger.error(message_no_header)
sys.exit(1)
continue
# If no header found, error message and exit
if not column_order:
- logger.error("ERROR: It seems that your info file does not have a header, or "
- "this header does not have, at least, the required columns"
- "separated: to_annotate, gsize nb_conts and L90 (in any order).\n")
+ logger.error(message_no_header)
sys.exit(1)
# Get all information on the given genome
# line.strip().split() -> all given information.
@@ -758,42 +752,36 @@ def read_genomes_info(list_file, name, date, dbpath, dbpath2):
try:
infos = line.strip().split()
# Get genome name with its path to db_dir
- gname = infos[column_order["to_annotate"]]
- gpath = os.path.join(dbpath, gname)
+ gpath = infos[column_order["to_annotate"]]
gsize = int(infos[column_order["gsize"]])
gl90 = int(infos[column_order["L90"]])
gcont = int(infos[column_order["nb_conts"]])
# If invalid values, warning message and ignore genome
except ValueError:
- 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))
+ logger.warning(f"For genome {gname}, at least one of your columns 'gsize', "
+ "'nb_conts' or 'L90' contains a non numeric character. "
+ "This genome will be ignored.")
continue
# If no value for at least 1 field, warning message and ignore genome
except IndexError:
- logger.error("ERROR: Check that all fields of {} are filled in each "
- "line (can be 'NA')".format(list_file))
- sys.exit(-1)
-
+ logger.error("ERROR: Check that all fields of {list_file} are filled in each "
+ "line (can be 'NA')")
+ sys.exit(1)
# Could we find genome file?
# Check if genome file exists in db_path.
if not os.path.isfile(gpath):
- if dbpath2:
- # If it does not exist, and there is a 2nd db_path, check if it exists there
- gpath = os.path.join(dbpath2, gname)
- # If still not in db_path2, warning message and ignore genome
- if not os.path.isfile(gpath):
- logger.warning("{} genome file does not exist in the given "
- "database {} nor in the other directory ({}). "
- "It will be ignored.".format(gname, dbpath, dbpath2))
- continue
- else:
- logger.warning("{} genome file does not exist in the given "
- "database {}. It will be ignored.".format(gname, dbpath))
- continue
+ logger.warning(f"{gpath} genome file does not exist. This genome will be ignored.")
+ continue
# cur genome information to save:
# [spegenus.date, path_orig_seq, path_to_sequence_to_annotate, size, nbcont, l90]
- genomes[gname] = [spegenus, gpath, gpath, gsize, gcont, gl90]
+ if name and date:
+ genomes[gpath] = [spegenus, gpath, gpath, gsize, gcont, gl90]
+ # If called from prepare, no need to rename genomes
+ else:
+ gfile = os.path.basename(gpath)
+ gname = os.path.splitext(gfile)[0]
+ genomes[gfile] = [gname, gpath, gpath, gsize, gcont, gl90]
+ logger.info(("Found {} genomes in total").format(len(genomes)))
return genomes
@@ -1155,6 +1143,7 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
return contigs, sizes
+
def logger_thread(q):
"""
Queue listener used in a thread to handle the logs put to a QueueHandler