From 2e8d2e9d4540df069ed1fc8605fa8698089d0d20 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 2 Sep 2020 11:48:28 +0200
Subject: [PATCH] output directory required
---
PanACoTA/subcommands/corepers.py | 10 +++-------
PanACoTA/subcommands/tree.py | 6 +++---
2 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/PanACoTA/subcommands/corepers.py b/PanACoTA/subcommands/corepers.py
index e22edcd4..ad60a87c 100755
--- a/PanACoTA/subcommands/corepers.py
+++ b/PanACoTA/subcommands/corepers.py
@@ -185,7 +185,9 @@ def build_parser(parser):
required = parser.add_argument_group('Required arguments')
required.add_argument("-p", dest="pangenome", required=True,
help="PanGenome file (1 line per family, first column is fam number)")
-
+ required.add_argument("-o", dest="outputdir", required=True,
+ help=("Specify the output directory for your core/persistent genome."),
+ default=".")
optional = parser.add_argument_group('Optional arguments')
optional.add_argument("-t", "--tol", dest="tol", default=1, type=percentage,
help=("min %% of genomes having at least 1 member in a family to "
@@ -207,12 +209,6 @@ def build_parser(parser):
"only 1 member exactly is allowed. This option is not compatible "
"with -M (which is allowing multigenic families: having several "
"members in any number of genomes).")
- optional.add_argument("-o", dest="outputdir",
- help=("You can specify an output directory for your core/persistent genome. "
- "By default, it will be saved in the current directory. "
- "Your output file will be named: "
- "PersGenome_<pangenome_filename>_tol[-multi][-mixed].lst"),
- default=".")
optional.add_argument("-F", dest="floor", action="store_true",
help="When you specify the '-tol' option, with a number lower "
"than 1, you can add this option to use floor('tol'*N) "
diff --git a/PanACoTA/subcommands/tree.py b/PanACoTA/subcommands/tree.py
index 6a62d6b1..9ea6e9fb 100755
--- a/PanACoTA/subcommands/tree.py
+++ b/PanACoTA/subcommands/tree.py
@@ -159,6 +159,8 @@ def build_parser(parser):
required.add_argument("-a", dest="alignment", required=True,
help=("Alignment file in multi-fasta: each header will be a "
"leaf of the inferred tree."))
+ required.add_argument("-o", dest="outdir", required=True,
+ help=("Directory where tree results will be saved. "))
# Choose with which soft inferring phylogenetic tree
softparse = parser.add_argument_group('Choose soft to use (default is IQtree)')
@@ -172,9 +174,7 @@ def build_parser(parser):
help=("Indicate how many bootstraps you want to compute. By "
"default, no bootstrap is calculated. For IQtree, it "
"will use ultrafast bootstrap (>=1000)."))
- optional.add_argument("-o", dest="outdir", default=".",
- help=("Directory where tree results will be saved. "
- "By default, it is saved in the current directory."))
+
optional.add_argument("--threads", dest="threads", default=1, type=thread_num,
help=("add this option if you want to parallelize on several threads. "
"Indicate on how many threads you want to parallelize. "
--
GitLab