Correct some typos

docs/userguide.rst

@@ -6,7 +6,7 @@ User Guide
 Overview
 ========
 
-You can use **Rapide Peptide Generator** using the standalone called::
+You can run **Rapide Peptide Generator** using the standalone called::
 
     rpg
 

rpg/RapidPeptidesGenerator.py

@@ -231,7 +231,7 @@ def main():
                                                  "sequential or concurrent (-d"
                                                  " option). Resulting peptides"
                                                  " are outputted in a file (-o"
-                                                 " option) if fasta, csv or ts"
+                                                 " option) in fasta, csv or ts"
                                                  "v format (-f option). Classi"
                                                  "cal enzymes are included (-l"
                                                  " option to print available e"

rpg/rule.py

@@ -205,7 +205,7 @@ class Rule:
         # First comment
         else:
             ret_com += "Always" if self.cut else "Never"
-            ret_com += " cut "
+            ret_com += " cleaves "
             ret_com += "after " if self.pos > 0 else "before "
             ret_com += self.letter
             ret_com += ", except..."

tests/test_enzyme.py

@@ -49,14 +49,16 @@ def test_enzyme(tmpdir):
     all_rules = rule.create_rules(dict_rule)
     new_enz = enzyme.Enzyme(-1, "fake_enzyme", all_rules)
     new_enz.write_enzyme_in_user_file(str(output_file))
-    assert output_file.read() == '\n\n\n# User-defined enzyme fake_enzyme\nENZ = []\n'\
-                         '\nE_1 = rule.Rule(0, "E", False, 1) # Never cut '\
-                         'after E, except...\nD_E_1M1 = rule.Rule(-1, "D", '\
-                         'True, -1) # Always cut after E, preceded by D, '\
-                         'except...\nE_1.rules.append(D_E_1M1)\nENZ.append('\
-                         'E_1)\n\nENZYME = enzyme.Enzyme(CPT_ENZ, "fake_enzym'\
-                         'e", ENZ, 0)\n# Add it to available enzymes\nAVAILAB'\
-                         'LE_ENZYMES_USER.append(ENZYME)\nCPT_ENZ += 1\n'
+    assert output_file.read() == '\n\n\n# User-defined enzyme fake_enzyme\nEN'\
+                                 'Z = []\n\nE_1 = rule.Rule(0, "E", False, 1)'\
+                                 ' # Never cleaves after E, except...\nD_E_1M'\
+                                 '1 = rule.Rule(-1, "D", True, -1) # Always c'\
+                                 'leaves after E, preceded by D, except...\nE'\
+                                 '_1.rules.append(D_E_1M1)\nENZ.append(E_1)\n'\
+                                 '\nENZYME = enzyme.Enzyme(CPT_ENZ, "fake_enz'\
+                                 'yme", ENZ, 0)\n# Add it to available enzyme'\
+                                 's\nAVAILABLE_ENZYMES_USER.append(ENZYME)\nC'\
+                                 'PT_ENZ += 1\n'
 
 def test_check_enzyme_name():
     """Test function 'check_enzyme_name(name_new_enz, all_name_enz)'."""

tests/test_rule.py

@@ -71,18 +71,18 @@ def test_rule():
     prev_com = " # "
     # Test function 'format_a_rule(prev_name, prev_com)'
     res = rule2.format_a_rule(prev_name, prev_com)
-    assert res == ['D_0', ' # Always cut before D, except...',
-                   'D_0 = rule.Rule(0, "D", True, 0) # Always cut before D, '
+    assert res == ['D_0', ' # Always cleaves before D, except...',
+                   'D_0 = rule.Rule(0, "D", True, 0) # Always cleaves before D, '
                    'except...']
     res = rule1.format_a_rule(prev_name, prev_com)
-    assert res == ['1Q2', ' # Never cut after Q, except...',
-                   '1Q2 = rule.Rule(2, "Q", False, 1) # Never cut after Q, '
+    assert res == ['1Q2', ' # Never cleaves after Q, except...',
+                   '1Q2 = rule.Rule(2, "Q", False, 1) # Never cleaves after Q, '
                    'except...']
 
     # Test function 'format_rule()'
     res = rule2.format_rule()
-    assert res == 'D_0 = rule.Rule(0, "D", True, 0) # Always cut before D, ex'\
-                  'cept...\nD_0Q2 = rule.Rule(2, "Q", False, 1) # Never cut b'\
+    assert res == 'D_0 = rule.Rule(0, "D", True, 0) # Always cleaves before D, ex'\
+                  'cept...\nD_0Q2 = rule.Rule(2, "Q", False, 1) # Never cleaves b'\
                   'efore D, followed by Q, except...\nD_0.rules.append(D_0Q2)'\
                   '\nENZ.append(D_0)\n\n'
 
@@ -328,15 +328,15 @@ def test_create_rules():
     assert len(res) == 3
 
     # Other complexe rule
-    # Don't cut after E if there is a D before
-    # But cut after E otherwise
+    # Don't cleaves after E if there is a D before
+    # But cleaves after E otherwise
     rule3 = "(E,)"
     all_rules[rule3] = True
     exc3 = "(D)(E,)"
     all_rules[exc3] = False
     # Truth for rule3
     truth3_1 = rule.Rule(-1, "D", False, -1)
-    truth3 = rule.Rule(0, "E", True, 1)  # Cut after E
+    truth3 = rule.Rule(0, "E", True, 1)  # cleaves after E
     truth3.rules.append(truth3_1)
     res = rule.create_rules(all_rules)
     assert truth1 in res
@@ -346,13 +346,13 @@ def test_create_rules():
     assert len(res) == 4
 
     # Similar complexe rule
-    # Cut after G if there is a F before
-    # But don't cut after G otherwise
+    # Cleaves after G if there is a F before
+    # But don't cleaves after G otherwise
     rule4 = "(F)(G,)"
     all_rules[rule4] = True
     # Truth for rule4
     truth4_1 = rule.Rule(-1, "F", True, -1)
-    truth4 = rule.Rule(0, "G", False, 1)  # Don't cut after G
+    truth4 = rule.Rule(0, "G", False, 1)  # Don't cleaves after G
     truth4.rules.append(truth4_1)
     res = rule.create_rules(all_rules)
     assert truth1 in res
@@ -374,7 +374,7 @@ def test_create_rules():
     assert len(res) == 7
 
     # Double comma and 'or'
-    # Cut after I or J, except if a K is after, but cut if a L is before
+    # Cleaves after I or J, except if a K is after, but cleaves if a L is before
     all_rules = {}
     rule6 = "(,I or J,)"
     all_rules[rule6] = True