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Nicolas MAILLET
rpg
Commits
d8488b53
Commit
d8488b53
authored
Apr 30, 2018
by
Nicolas MAILLET
Browse files
change miss-cleavage to miscleavage
parent
b73ad5cb
Changes
3
Hide whitespace changes
Inline
Side-by-side
tests/test_RapidPeptidesGenerator.py
View file @
d8488b53
...
...
@@ -9,14 +9,14 @@ def test_restricted_float(capsys):
with
pytest
.
raises
(
SystemExit
)
as
pytest_wrapped_e
:
RapidPeptidesGenerator
.
restricted_float
(
-
10
)
_
,
err
=
capsys
.
readouterr
()
assert
err
==
"Value Error: mis
s-
cleavage value should be between 0 and "
\
assert
err
==
"Value Error: miscleavage value should be between 0 and "
\
"100.
\n
"
assert
pytest_wrapped_e
.
type
==
SystemExit
assert
pytest_wrapped_e
.
value
.
code
==
1
with
pytest
.
raises
(
SystemExit
)
as
pytest_wrapped_e
:
RapidPeptidesGenerator
.
restricted_float
(
"z"
)
_
,
err
=
capsys
.
readouterr
()
assert
err
==
"Type Error: mis
s-
cleavage value should be a float between"
\
assert
err
==
"Type Error: miscleavage value should be a float between"
\
" 0 and 100.
\n
"
assert
pytest_wrapped_e
.
type
==
SystemExit
assert
pytest_wrapped_e
.
value
.
code
==
1
...
...
@@ -73,7 +73,7 @@ def test_create_enzymes_to_use(capsys):
miss_cleavage
=
[
1.1
,
20
,
40
]
res
=
RapidPeptidesGenerator
.
create_enzymes_to_use
(
enzymes
,
miss_cleavage
)
_
,
err
=
capsys
.
readouterr
()
assert
err
==
"Warning: Too much mis
s-
cleavage values. Last values will "
\
assert
err
==
"Warning: Too much miscleavage values. Last values will "
\
"be ignored.
\n
"
assert
res
.
__repr__
()
==
"[Id: 19
\n
Name: Glu-C
\n
Ratio Miss Cleaveage: 1.1"
\
"0%
\n
Rules: [index=0
\n
letter=D
\n
cut=True
\n
pos=1
\n
,"
\
...
...
tests/test_core.py
View file @
d8488b53
...
...
@@ -166,7 +166,7 @@ def test_output_results(capsys, tmpdir):
"8,5.54,F
\n
"
# Verbose > 2
assert
out
==
"
\n
Number of cleavage: 4
\n
Cleavage position: 4, 7, 12, 15
\n
"
\
"Number of mis
s-
cleavage: 0
\n
M
is
s-
cleavage position:
\n
Miss"
\
"Number of miscleavage: 0
\n
m
iscleavage position:
\n
Miss"
\
"-cleavage ratio: 0.00%
\n
Smallest peptide size: 1
\n
N termin"
\
"al peptide: WQSD
\n
C terminal peptide: F
\n
"
+
\
output_file
.
read
()
...
...
tests/test_digest.py
View file @
d8488b53
...
...
@@ -21,8 +21,8 @@ def test_resultonedigestion():
# Test function '__repr__()'
res_dig0
=
digest
.
ResultOneDigestion
(
enz_name
,
peptides
,
nb_cleav
,
pos_mc
)
assert
res_dig0
.
__repr__
()
==
"Number of cleavage: 1
\n
Number of miss-clea"
\
"vage: 2
\n
Positions of mis
s-
cleavage: [2, 3"
\
"]
\n
Ratio of mis
s-
cleavage: 66.666666666666"
\
"vage: 2
\n
Positions of miscleavage: [2, 3"
\
"]
\n
Ratio of miscleavage: 66.666666666666"
\
"66
\n
Peptides: [Original header: Test
\n
No. "
\
"peptide: 0
\n
Enzyme: fake_enzyme
\n
Cleav. po"
\
"s: 3
\n
Pep. size: 8
\n
Pep. mass: 1012.98488"
\
...
...
@@ -114,8 +114,8 @@ def test_resultonedigestion():
# Test function 'get_more_info()'
assert
res_dig5
.
get_more_info
()
==
"
\n
Number of cleavage: 5
\n
Cleavage pos"
\
"ition: 3, 4, 3
\n
Number of miss-cleava"
\
"ge: 6
\n
M
is
s-
cleavage position: 2, 3, "
\
"4, 6, 2, 3
\n
M
is
s-
cleavage ratio: "
\
"ge: 6
\n
m
iscleavage position: 2, 3, "
\
"4, 6, 2, 3
\n
m
iscleavage ratio: "
\
"54.55%
\n
Smallest peptide size: 8
\n
N t"
\
"erminal peptide: QWSDESDF
\n
C terminal"
\
" peptide: QWSDESDF"
...
...
@@ -345,8 +345,8 @@ def test_digest_from_input(capsys, tmpdir):
seq
=
"WQSDESDFZQSDESDF"
res
=
digest
.
digest_from_input
(
seq
,
enzymes
,
mode
)
assert
res
[
0
][
0
].
__repr__
()
==
"Number of cleavage: 4
\n
Number of miss-cle"
\
"avage: 0
\n
Positions of mis
s-
cleavage: []"
\
"
\n
Ratio of mis
s-
cleavage: 0.0
\n
Peptides: "
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0.0
\n
Peptides: "
\
"[Original header: Input
\n
No. peptide: 0"
\
"
\n
Enzyme: fake_enzyme1
\n
Cleav. pos: 4
\n
Pe"
\
"p. size: 4
\n
Pep. mass: 534.52598
\n
Pep. pI"
\
...
...
@@ -371,8 +371,8 @@ def test_digest_from_input(capsys, tmpdir):
fasta_file
.
write
(
">Fake1
\n
WQSDESDFZQS
\n
DESDF
\n
>Fake2
\n
NPHARDORCOMPLET"
)
res
=
digest
.
digest_from_input
(
str
(
fasta_file
),
enzymes
,
mode
)
assert
res
[
0
][
0
].
__repr__
()
==
"Number of cleavage: 4
\n
Number of miss-cle"
\
"avage: 0
\n
Positions of mis
s-
cleavage: []"
\
"
\n
Ratio of mis
s-
cleavage: 0.0
\n
Peptides: "
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0.0
\n
Peptides: "
\
"[Original header: Fake1
\n
No. peptide: 0
\n
"
\
"Enzyme: fake_enzyme1
\n
Cleav. pos: 4
\n
Pep."
\
" size: 4
\n
Pep. mass: 534.52598
\n
Pep. pI: "
\
...
...
@@ -392,8 +392,8 @@ def test_digest_from_input(capsys, tmpdir):
" 16
\n
Pep. size: 1
\n
Pep. mass: 165.19188
\n
"
\
"Pep. pI: 5.54
\n
Sequence: F
\n
]
\n
"
assert
res
[
1
][
0
].
__repr__
()
==
"Number of cleavage: 0
\n
Number of miss-cle"
\
"avage: 0
\n
Positions of mis
s-
cleavage: []"
\
"
\n
Ratio of mis
s-
cleavage: 0
\n
Peptides: [O"
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0
\n
Peptides: [O"
\
"riginal header: Fake2
\n
No. peptide: 0
\n
En"
\
"zyme: fake_enzyme1
\n
Cleav. pos: 0
\n
Pep. s"
\
"ize: 15
\n
Pep. mass: 2014.35098
\n
Pep. pI: "
\
...
...
@@ -405,8 +405,8 @@ def test_digest_from_input(capsys, tmpdir):
"ke2
\n
NPHARDORCOMPLET
\n
+Fake2
\n
nNPHARDORCOMPLET
\n
"
)
res
=
digest
.
digest_from_input
(
str
(
fastq_file
),
enzymes
,
mode
)
assert
res
[
0
][
0
].
__repr__
()
==
"Number of cleavage: 4
\n
Number of miss-cle"
\
"avage: 0
\n
Positions of mis
s-
cleavage: []"
\
"
\n
Ratio of mis
s-
cleavage: 0.0
\n
Peptides: "
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0.0
\n
Peptides: "
\
"[Original header: Fake1
\n
No. peptide: 0
\n
"
\
"Enzyme: fake_enzyme1
\n
Cleav. pos: 4
\n
Pep."
\
" size: 4
\n
Pep. mass: 534.52598
\n
Pep. pI: "
\
...
...
@@ -426,8 +426,8 @@ def test_digest_from_input(capsys, tmpdir):
" 16
\n
Pep. size: 1
\n
Pep. mass: 165.19188
\n
"
\
"Pep. pI: 5.54
\n
Sequence: F
\n
]
\n
"
assert
res
[
1
][
0
].
__repr__
()
==
"Number of cleavage: 0
\n
Number of miss-cle"
\
"avage: 0
\n
Positions of mis
s-
cleavage: []"
\
"
\n
Ratio of mis
s-
cleavage: 0
\n
Peptides: [O"
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0
\n
Peptides: [O"
\
"riginal header: Fake2
\n
No. peptide: 0
\n
En"
\
"zyme: fake_enzyme1
\n
Cleav. pos: 0
\n
Pep. s"
\
"ize: 15
\n
Pep. mass: 2014.35098
\n
Pep. pI: "
\
...
...
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