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Commit 47076e6b authored by Amandine  PERRIN's avatar Amandine PERRIN
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add run tree module to all_modules

parent df7c68bc
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Pipeline #40031 passed
...@@ -89,7 +89,7 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l ...@@ -89,7 +89,7 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l
if verbose >= 15: if verbose >= 15:
level = logging.DEBUG level = logging.DEBUG
logfile_base = os.path.join(outdir, "PanACoTA-all_modules") 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) verbose=verbose, quiet=quiet)
logger = logging.getLogger('all_modules') logger = logging.getLogger('all_modules')
logger.info(f'PanACoTA version {version}') logger.info(f'PanACoTA version {version}')
...@@ -149,10 +149,31 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l ...@@ -149,10 +149,31 @@ def main(cmd, outdir, threads, NCBI_species_taxid, NCBI_species, levels, cutn, l
print(align_file) print(align_file)
# Tree step # 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") outdir_tree = os.path.join(outdir, "6-tree_module")
tree.main("PanACoTA tree", align_file, outdir_tree, soft, model, threads, boot=False, tree.main("PanACoTA tree", align_file, outdir_tree, soft, model, threads, boot=False,
write_boot=False, memory=False, fast=False, verbose=verbose, quiet=quiet) write_boot=False, memory=False, fast=False, verbose=verbose, quiet=quiet)
logger.info("All modules of PanACOTA are finished.")
def build_parser(parser): def build_parser(parser):
""" """
Method to create a parser for command-line options Method to create a parser for command-line options
......
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