From 89a7186bcd3de21a0fcf1b4ca35f7b5c33d6b5fb Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 22 Oct 2020 19:11:58 +0200
Subject: [PATCH] complete util functions
---
PanACoTA/utils.py | 4 +++-
PanACoTA/utils_argparse.py | 13 +++++++++++++
2 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index 9828d464..11a099d2 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -522,6 +522,8 @@ def write_lstinfo(list_file, genomes, outdir):
for genome, values in sorted(genomes.items(), key=sort_genomes_byname_l90_nbcont):
gembase, _, to_annote, gsize, nbcont, l90 = [str(x) for x in values]
outf.write("\t".join([gembase, genome, to_annote, gsize, nbcont, l90]) + "\n")
+ return outlst
+
def sort_genomes_by_name(x):
"""
@@ -943,7 +945,7 @@ def cat(list_files, output, title=None):
widgets = [title + ': ', progressbar.Bar(marker='â–ˆ', left='', right='', fill=' '),
' ', progressbar.Counter(), f"/{nbfiles}" ' (',
progressbar.Percentage(), ") - ", progressbar.Timer()]
- bar = progressbar.ProgressBar(widgets=widgets, max_value=nbfiles, term_width=100).start()
+ bar = progressbar.ProgressBar(widgets=widgets, max_value=nbfiles, term_width=79).start()
curnum = 1
with open(output, "w") as outf:
for file in list_files:
diff --git a/PanACoTA/utils_argparse.py b/PanACoTA/utils_argparse.py
index 8f07f939..8882571a 100644
--- a/PanACoTA/utils_argparse.py
+++ b/PanACoTA/utils_argparse.py
@@ -43,6 +43,7 @@ April 2017
from PanACoTA import utils
import argparse
+
def gen_name(param):
if not utils.check_format(param):
msg = ("The genome name must contain 4 characters. For example, this name can "
@@ -136,3 +137,15 @@ def percentage(param):
"be in [0, 1]. Invalid value: {}".format(param))
raise argparse.ArgumentTypeError(msg)
return param
+
+
+def perc_id(param):
+ try:
+ param = float(param)
+ except Exception:
+ msg = "argument -i percentage_id: invalid float value: {}".format(param)
+ raise argparse.ArgumentTypeError(msg)
+ if param < 0 or param > 1:
+ msg = ("The minimum %% of identity must be in [0, 1]. Invalid value: {}".format(param))
+ raise argparse.ArgumentTypeError(msg)
+ return param
--
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