From 7635c7b270cdc2d2c90a3fca6441183e7c241d2f Mon Sep 17 00:00:00 2001
From: Nicolas MAILLET <nicolas.maillet@pasteur.fr>
Date: Wed, 27 Jun 2018 17:06:35 +0200
Subject: [PATCH] correct funny typo
---
docs/userguide.rst | 4 ++--
rpg/RapidPeptidesGenerator.py | 12 ++++++------
rpg/digest.py | 2 +-
rpg/enzyme.py | 2 +-
tests/test_RapidPeptidesGenerator.py | 10 +++++-----
tests/test_enzyme.py | 2 +-
6 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/docs/userguide.rst b/docs/userguide.rst
index 929575a..d038271 100644
--- a/docs/userguide.rst
+++ b/docs/userguide.rst
@@ -164,7 +164,7 @@ Here are all available options in **RPG**:
**-l, -\\-list**: Display the list of available enzymes.
-**-m, -\\-misscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order as the -\\-enzymes options (*i.e.* -m 15 -m 5 -m 10). It works only for sequential digestion (default: 0). See :ref:`misscleavage` for more information.
+**-m, -\\-miscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order as the -\\-enzymes options (*i.e.* -m 15 -m 5 -m 10). It works only for sequential digestion (default: 0). See :ref:`miscleavage` for more information.
**-n, -\\-noninteractive**: Non-interactive mode. No standard output, only error(s) (-\\-quiet enable, overwrite -v). If output filename already exists, output file will be overwritten. See :ref:`nointer` for more information.
@@ -235,7 +235,7 @@ Here, we have to understand that 'afterP' cleaves at the same positions as in se
Default mode is 'sequential'. Reminder: you can input miscleavage values only for this mode.
-.. _misscleavage:
+.. _miscleavage:
Miscleavage
===========
diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py
index fc1100e..7156e49 100644
--- a/rpg/RapidPeptidesGenerator.py
+++ b/rpg/RapidPeptidesGenerator.py
@@ -265,7 +265,7 @@ def main():
"single protein sequence without commentary")
group_launch.add_argument("-l", "--list", action="store_true",
help="Display the list of available enzymes")
- parser.add_argument("-m", "--misscleavage", metavar="", default=[],
+ parser.add_argument("-m", "--miscleavage", metavar="", default=[],
action='append', type=restricted_float,
help="Percentage of miscleavage, between 0 and 100,"
" by enzyme(s). It should be in the same order than "
@@ -303,7 +303,7 @@ def main():
mode = "sequential"
if args.digest == "c" or args.digest == "concurrent":
mode = "concurrent"
- args.misscleavage = [] # No miscleavage on concurrent, infinite time
+ args.miscleavage = [] # No miscleavage on concurrent, infinite time
# --list option
if args.list:
@@ -351,14 +351,14 @@ def main():
else:
break
- # More miss cleavage than enzyme
- if len(args.misscleavage) > len(args.enzymes):
+ # More mis cleavage than enzyme
+ if len(args.miscleavage) > len(args.enzymes):
core.handle_errors("Too much miscleavage values. Last values will "
"be ignored.")
- args.misscleavage = args.misscleavage[:len(args.enzymes)]
+ args.miscleavage = args.miscleavage[:len(args.enzymes)]
# Get all enzymes inputed
- enzymes_to_use = get_enzymes_to_use(mode, args.enzymes, args.misscleavage)
+ enzymes_to_use = get_enzymes_to_use(mode, args.enzymes, args.miscleavage)
# Output options
if args.verbose:
diff --git a/rpg/digest.py b/rpg/digest.py
index ca94621..26d0068 100644
--- a/rpg/digest.py
+++ b/rpg/digest.py
@@ -186,7 +186,7 @@ class ResultOneDigestion:
def get_more_info(self):
"""Return informations and statistics about this digestion,
- *i.e.* number of (miss)-cleavages and positions, miscleavage
+ *i.e.* number of (mis)-cleavages and positions, miscleavage
ratio, size of the smallest peptide and first and last peptide.
:return: informations and statistics ready to be printed
diff --git a/rpg/enzyme.py b/rpg/enzyme.py
index b3ab07b..07eb420 100644
--- a/rpg/enzyme.py
+++ b/rpg/enzyme.py
@@ -59,7 +59,7 @@ class Enzyme:
# self representation for print
def __repr__(self):
- return "Id: %s\nName: %s\nRatio Miss Cleaveage: %.2f%%\nRules: %s\n" %\
+ return "Id: %s\nName: %s\nRatio Miscleavage: %.2f%%\nRules: %s\n" %\
(self.id_, self.name, self.ratio_miscleavage, self.rules)
# Equality between two Enzymes
diff --git a/tests/test_RapidPeptidesGenerator.py b/tests/test_RapidPeptidesGenerator.py
index 279620f..df7ef32 100644
--- a/tests/test_RapidPeptidesGenerator.py
+++ b/tests/test_RapidPeptidesGenerator.py
@@ -66,12 +66,12 @@ def test_create_enzymes_to_use(capsys):
enzymes = [23, 31, 29]
miscleavage = [1.1, 20]
res = RapidPeptidesGenerator.create_enzymes_to_use(enzymes, miscleavage)
- assert res.__repr__() == "[Id: 23\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
+ assert res.__repr__() == "[Id: 23\nName: Glu-C\nRatio Miscleavage: 1.1"\
"0%\nRules: [index=0\nletter=D\ncut=True\npos=1\n,"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 31"\
- "\nName: NTCB\nRatio Miss Cleaveage: 20.00%\nRules"\
+ "\nName: NTCB\nRatio Miscleavage: 20.00%\nRules"\
": [index=0\nletter=C\ncut=True\npos=0\n]\n, Id: "\
- "29\nName: Lys-N\nRatio Miss Cleaveage: 0.00%\nRul"\
+ "29\nName: Lys-N\nRatio Miscleavage: 0.00%\nRul"\
"es: [index=0\nletter=K\ncut=True\npos=0\n]\n]"
enzymes = [23, 31]
miscleavage = [1.1, 20, 40]
@@ -79,8 +79,8 @@ def test_create_enzymes_to_use(capsys):
_, err = capsys.readouterr()
assert err == "Warning: Too much miscleavage values. Last values will "\
"be ignored.\n"
- assert res.__repr__() == "[Id: 23\nName: Glu-C\nRatio Miss Cleaveage: 1.1"\
+ assert res.__repr__() == "[Id: 23\nName: Glu-C\nRatio Miscleavage: 1.1"\
"0%\nRules: [index=0\nletter=D\ncut=True\npos=1\n,"\
" index=0\nletter=E\ncut=True\npos=1\n]\n, Id: 31"\
- "\nName: NTCB\nRatio Miss Cleaveage: 20.00%\nRules"\
+ "\nName: NTCB\nRatio Miscleavage: 20.00%\nRules"\
": [index=0\nletter=C\ncut=True\npos=0\n]\n]"
diff --git a/tests/test_enzyme.py b/tests/test_enzyme.py
index 02b53e9..0b8fcc7 100644
--- a/tests/test_enzyme.py
+++ b/tests/test_enzyme.py
@@ -17,7 +17,7 @@ def test_enzyme(tmpdir):
# Test function '__repr__()'
res = enz0.__repr__()
- assert res == "Id: -1\nName: fake_enzyme1\nRatio Miss Cleaveage: 0.00%\nR"\
+ assert res == "Id: -1\nName: fake_enzyme1\nRatio Miscleavage: 0.00%\nR"\
"ules: [index=0\nletter=D\ncut=True\npos=1\n\tindex=-1\n\tl"\
"etter=S\n\tcut=False\n\tpos=-1\n]\n"
--
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