diff --git a/docs/userguide.rst b/docs/userguide.rst
index b493db50313ddfed7575d3b8bf61fd7fb25852ad..80b9994dff77414889148537c0deb56adfd9c589 100644
--- a/docs/userguide.rst
+++ b/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
diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py
index 5e9e1bbf48517a2f7ef5772a8b359fd519dc9cb5..3ab213252a665f0a83fd774cd9e0786bc7eb09a6 100644
--- a/rpg/RapidPeptidesGenerator.py
+++ b/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"
diff --git a/rpg/rule.py b/rpg/rule.py
index 233d008d7cf01cbd367d5ffcc376e9f0bcfe429c..8c1312dfd006d821aa391158dd286a7479c694d9 100644
--- a/rpg/rule.py
+++ b/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..."
diff --git a/tests/test_enzyme.py b/tests/test_enzyme.py
index 64363bb775fbf7e26761c31a48010e197d593af7..02b53e954af1577f30de24f78b3e641fc1487646 100644
--- a/tests/test_enzyme.py
+++ b/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)'."""
diff --git a/tests/test_rule.py b/tests/test_rule.py
index 16a5d06d169f4e6b8df8a1df6f7513b05fbfc6aa..7eb8c4122d71d07ccd93a2b1726e830d647c341d 100644
--- a/tests/test_rule.py
+++ b/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