diff --git a/PanACoTA/subcommands/all_modules.py b/PanACoTA/subcommands/all_modules.py
index 0e6bda3a66b5c3633e63e2644d1a2b03347f3d4e..6953dab84b153fcdc01154c01e6871ff1a8e0507 100644
--- a/PanACoTA/subcommands/all_modules.py
+++ b/PanACoTA/subcommands/all_modules.py
@@ -67,16 +67,22 @@ def main_from_parse(args):
result of argparse parsing of all arguments in command line
"""
cmd = "PanACoTA " + ' '.join(args.argv)
- main(cmd, args.outdir, args.threads, args.NCBI_species_taxid, args.NCBI_species,
- args.levels, args.cutn, args.l90, args.nbcont, args.name, args.prodigal_only, args.min_id,
- args.tol, args.multi, args.mixed, args.soft, verbose=args.verbose, quiet=args.quiet)
-
-
-def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l90, nbcont,
- name, prodigal_only, min_id, tol, multi, mixed, soft, verbose=0, quiet=False):
+ args_all = (args.outdir, args.threads, args.verbose, args.quiet)
+ args_prepare = (args.ncbi_species_taxid, args.ncbi_species, args.levels,
+ args.tmp_dir, args.no_refseq, args.db_dir, args.only_mash, args.info_file,
+ args.l90, args.nbcont, args.cutn, args.min_dist, args.max_dist)
+ args_annot = (args.name, args.qc_only, args.date, args.prodigal_only)
+ args_pan = (args.min_id, args.clust_mode, args.spedir, args.outfile)
+ args_cp = (args.tol, args.mixed, args.multi, args.floor)
+ args_tree = (args.soft, args.model, args.boot, args.write_boot, args.memory, args.fast)
+ main(cmd, args_all, args_prepare, args_annot, args_pan, args_cp, args_tree)
+
+
+def main(cmd, args_all, args_prepare, args_annot, args_pan, args_corepers, args_tree):
"""
Call all modules, one by one, using output of one as input for the next one
"""
+ outdir, threads, verbose, quiet = args_all
os.makedirs(outdir, exist_ok=True)
# Initialize logger
import logging
@@ -98,14 +104,9 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l
# Run prepare module
outdir_prepare = os.path.join(outdir, "1-prepare_module")
- tmp_dir = ""
- no_refseq = False
- db_dir = ""
- only_mash = False
- info_file = ""
- min_dist = 1e-4
- max_dist = 0.06
-
+ (NCBI_species_taxid, NCBI_species, levels, tmp_dir, no_refseq, db_dir, only_mash, info_file,
+ l90, nbcont, cutn, min_dist, max_dist) = args_prepare
+ logger.info("prepare step")
info_file = prepare.main("PanACoTA prepare", NCBI_species, NCBI_species_taxid, levels,
outdir_prepare, tmp_dir, threads, no_refseq, db_dir, only_mash,
info_file, l90, nbcont, cutn, min_dist, max_dist, verbose, quiet)
@@ -113,65 +114,49 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l
# Run annotate module
list_file = ""
db_path = ""
- outdir_annotate = os.path.join(outdir, "2-annotate_module")
- import time
- date = time.strftime("%m%y")
- force = False
- qc_only = False
tmp_dir = ""
+ force = False
+ outdir_annotate = os.path.join(outdir, "2-annotate_module")
+ (name, qc_only, date, prodigal_only) = args_annot
res_annot_dir = None
small = False
+ logger.info("annotate step")
lstinfo, nbgenomes = annotate.main("PanACoTA annotate", list_file, db_path, outdir_annotate,
name, date, l90, nbcont, cutn, threads, force, qc_only,
info_file, tmp_dir, res_annot_dir, verbose, quiet,
- prodigal_only, small)
+ prodigal_only)
# Pangenome step
name_pan = f"{name}_{nbgenomes}"
outdir_pan = os.path.join(outdir, "3-pangenome_module")
- clust_mode = 1
- spe_dir = ""
dbpath = os.path.join(outdir_annotate, "Proteins")
- panfile = pangenome.main("PanACoTA pangenome", lstinfo, name, dbpath, min_id, outdir_pan,
- clust_mode, spe_dir, threads, outfile=None, verbose=verbose,
+ (min_id, clust_mode, spe_dir, outfile) = args_pan
+ logger.info("pangenome step")
+ panfile = pangenome.main("PanACoTA pangenome", lstinfo, name_pan, dbpath, min_id, outdir_pan,
+ clust_mode, spe_dir, threads, outfile, verbose=verbose,
quiet=quiet)
# Coregenome step
outdir_corpers = os.path.join(outdir, "4-corepers_module")
+ logger.info("corepers step")
+ (tol, mixed, multi, floor) = args_corepers
corepers_file = corepers.main("PanACoTA corepers", panfile, tol, multi, mixed, outdir_corpers,
- verbose=verbose, quiet=quiet)
-
+ floor, verbose, quiet)
# Align step
outdir_align = os.path.join(outdir, "5-align_module")
force = False
+ logger.info("align step")
align_file = align.main("PanACoTA align", corepers_file, lstinfo, name_pan, outdir_annotate,
- outdir_align, threads, force, verbose, quiet)
- print(align_file)
+ outdir_align, threads, force, verbose=verbose, quiet=quiet)
+
# Tree step
- # models_fastme = {"p-distance": "p", "RY-symetric": "Y", "RY": "R",
- # "JC69": "J", "K2P": "K", "F81": "1", "F84": "4",
- # "TN93": "T", "LogDet": "L"}
- # models_fasttree = {"GTR": "-gtr", "JC": ""}
- # models_iqtree = set(["HKY", "JC", "F81", "K2P", "K3P", "K81uf",
- # "TNef", "TIM", "TIMef", "TVM", "TVMef", "SYM", "GTR"])
- # models_iqtree = {mod: mod for mod in models_iqtree}
- if soft == "fasttree":
- model = "-gtr"
- elif soft =="iqtree" or soft == "iqtree2":
- model = "GTR"
- elif soft == "quicktree":
- model = ""
- elif soft == "fastme":
- model = "T"
- else:
- logger.error(f"Soft {soft} is not possible.")
- sys.exit(1)
+ (soft, model, boot, write_boot, memory, fast) = args_tree
outdir_tree = os.path.join(outdir, "6-tree_module")
- tree.main("PanACoTA tree", align_file, outdir_tree, soft, model, threads, boot=False,
- write_boot=False, memory=False, fast=False, verbose=verbose, quiet=quiet)
-
+ logger.info("tree step")
+ tree.main("PanACoTA tree", align_file, outdir_tree, soft, model, threads, boot,
+ write_boot, memory, fast, verbose=verbose, quiet=quiet)
logger.info("All modules of PanACOTA are finished.")