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Nicolas MAILLET
rpg
Commits
24c9cf56
Commit
24c9cf56
authored
Apr 30, 2018
by
Nicolas MAILLET
Browse files
change miss-cleavage to miscleavage
parent
4bfe2279
Changes
1
Hide whitespace changes
Inline
Side-by-side
tests/test_digest.py
View file @
24c9cf56
...
...
@@ -20,7 +20,7 @@ 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 mis
s-
clea"
\
assert
res_dig0
.
__repr__
()
==
"Number of cleavage: 1
\n
Number of misclea"
\
"vage: 2
\n
Positions of miscleavage: [2, 3"
\
"]
\n
Ratio of miscleavage: 66.666666666666"
\
"66
\n
Peptides: [Original header: Test
\n
No. "
\
...
...
@@ -113,7 +113,7 @@ 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 mis
s-
cleava"
\
"ition: 3, 4, 3
\n
Number of miscleava"
\
"ge: 6
\n
miscleavage position: 2, 3, "
\
"4, 6, 2, 3
\n
miscleavage ratio: "
\
"54.55%
\n
Smallest peptide size: 8
\n
N t"
\
...
...
@@ -344,7 +344,7 @@ def test_digest_from_input(capsys, tmpdir):
# Test input data
seq
=
"WQSDESDFZQSDESDF"
res
=
digest
.
digest_from_input
(
seq
,
enzymes
,
mode
)
assert
res
[
0
][
0
].
__repr__
()
==
"Number of cleavage: 4
\n
Number of mis
s-
cle"
\
assert
res
[
0
][
0
].
__repr__
()
==
"Number of cleavage: 4
\n
Number of miscle"
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0.0
\n
Peptides: "
\
"[Original header: Input
\n
No. peptide: 0"
\
...
...
@@ -370,7 +370,7 @@ def test_digest_from_input(capsys, tmpdir):
fasta_file
=
tmpdir
.
join
(
"test.fasta"
)
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 mis
s-
cle"
\
assert
res
[
0
][
0
].
__repr__
()
==
"Number of cleavage: 4
\n
Number of miscle"
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0.0
\n
Peptides: "
\
"[Original header: Fake1
\n
No. peptide: 0
\n
"
\
...
...
@@ -391,7 +391,7 @@ def test_digest_from_input(capsys, tmpdir):
"ide: 4
\n
Enzyme: fake_enzyme1
\n
Cleav. pos:"
\
" 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 mis
s-
cle"
\
assert
res
[
1
][
0
].
__repr__
()
==
"Number of cleavage: 0
\n
Number of miscle"
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0
\n
Peptides: [O"
\
"riginal header: Fake2
\n
No. peptide: 0
\n
En"
\
...
...
@@ -404,7 +404,7 @@ def test_digest_from_input(capsys, tmpdir):
fastq_file
.
write
(
"@Fake1
\n
WQSDESDFZQSDESDF
\n
+Fake1
\n
nWQSDESDFZQSDESDF
\n
@Fa"
\
"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 mis
s-
cle"
\
assert
res
[
0
][
0
].
__repr__
()
==
"Number of cleavage: 4
\n
Number of miscle"
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0.0
\n
Peptides: "
\
"[Original header: Fake1
\n
No. peptide: 0
\n
"
\
...
...
@@ -425,7 +425,7 @@ def test_digest_from_input(capsys, tmpdir):
"ide: 4
\n
Enzyme: fake_enzyme1
\n
Cleav. pos:"
\
" 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 mis
s-
cle"
\
assert
res
[
1
][
0
].
__repr__
()
==
"Number of cleavage: 0
\n
Number of miscle"
\
"avage: 0
\n
Positions of miscleavage: []"
\
"
\n
Ratio of miscleavage: 0
\n
Peptides: [O"
\
"riginal header: Fake2
\n
No. peptide: 0
\n
En"
\
...
...
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