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Nicolas MAILLET
rpg
Commits
8aae8e79
Commit
8aae8e79
authored
May 04, 2018
by
Nicolas MAILLET
Browse files
Correct some typos
parent
5f43174f
Changes
5
Hide whitespace changes
Inline
Side-by-side
docs/userguide.rst
View file @
8aae8e79
...
...
@@ -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
View file @
8aae8e79
...
...
@@ -231,7 +231,7 @@ def main():
"sequential or concurrent (-d"
" option). Resulting peptides"
" are outputted in a file (-o"
" option) i
f
fasta, csv or ts"
" option) i
n
fasta, csv or ts"
"v format (-f option). Classi"
"cal enzymes are included (-l"
" option to print available e"
...
...
rpg/rule.py
View file @
8aae8e79
...
...
@@ -205,7 +205,7 @@ class Rule:
# First comment
else
:
ret_com
+=
"Always"
if
self
.
cut
else
"Never"
ret_com
+=
" c
ut
"
ret_com
+=
" c
leaves
"
ret_com
+=
"after "
if
self
.
pos
>
0
else
"before "
ret_com
+=
self
.
letter
ret_com
+=
", except..."
...
...
tests/test_enzyme.py
View file @
8aae8e79
...
...
@@ -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
\n
ENZ = []
\n
'
\
'
\n
E_1 = rule.Rule(0, "E", False, 1) # Never cut '
\
'after E, except...
\n
D_E_1M1 = rule.Rule(-1, "D", '
\
'True, -1) # Always cut after E, preceded by D, '
\
'except...
\n
E_1.rules.append(D_E_1M1)
\n
ENZ.append('
\
'E_1)
\n\n
ENZYME = enzyme.Enzyme(CPT_ENZ, "fake_enzym'
\
'e", ENZ, 0)
\n
# Add it to available enzymes
\n
AVAILAB'
\
'LE_ENZYMES_USER.append(ENZYME)
\n
CPT_ENZ += 1
\n
'
assert
output_file
.
read
()
==
'
\n\n\n
# User-defined enzyme fake_enzyme
\n
EN'
\
'Z = []
\n\n
E_1 = rule.Rule(0, "E", False, 1)'
\
' # Never cleaves after E, except...
\n
D_E_1M'
\
'1 = rule.Rule(-1, "D", True, -1) # Always c'
\
'leaves after E, preceded by D, except...
\n
E'
\
'_1.rules.append(D_E_1M1)
\n
ENZ.append(E_1)
\n
'
\
'
\n
ENZYME = enzyme.Enzyme(CPT_ENZ, "fake_enz'
\
'yme", ENZ, 0)
\n
# Add it to available enzyme'
\
's
\n
AVAILABLE_ENZYMES_USER.append(ENZYME)
\n
C'
\
'PT_ENZ += 1
\n
'
def
test_check_enzyme_name
():
"""Test function 'check_enzyme_name(name_new_enz, all_name_enz)'."""
...
...
tests/test_rule.py
View file @
8aae8e79
...
...
@@ -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 c
ut
before D, except...'
,
'D_0 = rule.Rule(0, "D", True, 0) # Always c
ut
before D, '
assert
res
==
[
'D_0'
,
' # Always c
leaves
before D, except...'
,
'D_0 = rule.Rule(0, "D", True, 0) # Always c
leaves
before D, '
'except...'
]
res
=
rule1
.
format_a_rule
(
prev_name
,
prev_com
)
assert
res
==
[
'1Q2'
,
' # Never c
ut
after Q, except...'
,
'1Q2 = rule.Rule(2, "Q", False, 1) # Never c
ut
after Q, '
assert
res
==
[
'1Q2'
,
' # Never c
leaves
after Q, except...'
,
'1Q2 = rule.Rule(2, "Q", False, 1) # Never c
leaves
after Q, '
'except...'
]
# Test function 'format_rule()'
res
=
rule2
.
format_rule
()
assert
res
==
'D_0 = rule.Rule(0, "D", True, 0) # Always c
ut
before D, ex'
\
'cept...
\n
D_0Q2 = rule.Rule(2, "Q", False, 1) # Never c
ut
b'
\
assert
res
==
'D_0 = rule.Rule(0, "D", True, 0) # Always c
leaves
before D, ex'
\
'cept...
\n
D_0Q2 = rule.Rule(2, "Q", False, 1) # Never c
leaves
b'
\
'efore D, followed by Q, except...
\n
D_0.rules.append(D_0Q2)'
\
'
\n
ENZ.append(D_0)
\n\n
'
...
...
@@ -328,15 +328,15 @@ def test_create_rules():
assert
len
(
res
)
==
3
# Other complexe rule
# Don't c
ut
after E if there is a D before
# But c
ut
after E otherwise
# Don't c
leaves
after E if there is a D before
# But c
leaves
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
# C
ut
after G if there is a F before
# But don't c
ut
after G otherwise
# C
leaves
after G if there is a F before
# But don't c
leaves
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 c
ut
after G
truth4
=
rule
.
Rule
(
0
,
"G"
,
False
,
1
)
# Don't c
leaves
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'
# C
ut
after I or J, except if a K is after, but c
ut
if a L is before
# C
leaves
after I or J, except if a K is after, but c
leaves
if a L is before
all_rules
=
{}
rule6
=
"(,I or J,)"
all_rules
[
rule6
]
=
True
...
...
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