correct funny typo

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
 ===========

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:

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

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

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]"

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"