diff --git a/PanACoTA/subcommands/all_modules.py b/PanACoTA/subcommands/all_modules.py index 835d2684589305d6643ab57a79399d68c4bab363..62fb3fa7476c4b1374a1605d3f3b268534a5e471 100644 --- a/PanACoTA/subcommands/all_modules.py +++ b/PanACoTA/subcommands/all_modules.py @@ -89,7 +89,7 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l if verbose >= 15: level = logging.DEBUG logfile_base = os.path.join(outdir, "PanACoTA-all_modules") - logfile_base = utils.init_logger(logfile_base, level, name='all_modules', log_details=True, + logfile_base = utils.init_logger(logfile_base, level, name='all_modules', verbose=verbose, quiet=quiet) logger = logging.getLogger('all_modules') logger.info(f'PanACoTA version {version}') @@ -149,10 +149,31 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l print(align_file) # 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) 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("All modules of PanACOTA are finished.") + + def build_parser(parser): """ Method to create a parser for command-line options