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chipseq_analysis
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BICF
Astrocyte
chipseq_analysis
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80514965
Commit
80514965
authored
5 years ago
by
Venkat Malladi
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Add in tests for checking single control se and pe.
parent
1c72ff6c
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1 merge request
!63
Resolve "Single Rep Pool and Pseudo"
Pipeline
#6187
failed with stages
in 5 seconds
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test_data/A_1.bedpe.gz
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test_data/A_1.bedpe.gz
test_data/B_1.bedpe.gz
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test_data/B_1.bedpe.gz
workflow/tests/test_pool_and_psuedoreplicate.py
+17
-2
17 additions, 2 deletions
workflow/tests/test_pool_and_psuedoreplicate.py
with
17 additions
and
2 deletions
test_data/A_1.bedpe.gz
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test_data/B_1.bedpe.gz
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workflow/tests/test_pool_and_psuedoreplicate.py
+
17
−
2
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80514965
...
...
@@ -33,8 +33,11 @@ def design_experiment_2(design_experiment):
@pytest.fixture
def
design_experiment_3
(
design_experiment
):
# Update second control to be same as first
design_experiment
.
loc
[
1
,
'
control_tag_align
'
]
=
'
B_1.bedse.gz
'
# Drop Replicate A_2
design_df
=
design_experiment
.
drop
(
design_experiment
.
index
[
1
])
# Update to be paired as first
design_experiment
.
loc
[
0
,
'
control_tag_align
'
]
=
'
B_1.bedpe.gz
'
design_experiment
.
loc
[
0
,
'
ttag_align
'
]
=
'
A_1.bedpe.gz
'
return
design_experiment
...
...
@@ -71,6 +74,18 @@ def test_single_rep(design_experiment_2):
shutil
.
copy
(
test_design_path
+
'
B_1.tagAlign.gz
'
,
cwd
)
single_rep
=
pool_and_psuedoreplicate
.
generate_design
(
'
false
'
,
1.2
,
design_experiment_2
,
cwd
,
1
,
1
)
assert
single_rep
.
shape
[
0
]
==
4
assert
len
(
single_rep
[
'
control_tag_align
'
].
unique
())
==
1
assert
single_rep
[
'
control_tag_align
'
].
unique
()[
0
]
==
'
B_1.tagAlign.gz
'
@pytest.mark.unit
def
test_single_control
(
design_experiment_3
):
cwd
=
os
.
getcwd
()
shutil
.
copy
(
test_design_path
+
'
A_1.bedpe.gz
'
,
cwd
)
shutil
.
copy
(
test_design_path
+
'
B_1.bedpe.gz
'
,
cwd
)
shutil
.
copy
(
test_design_path
+
'
A_1.tagAlign.gz
'
,
cwd
)
single_control
=
pool_and_psuedoreplicate
.
generate_design
(
'
true
'
,
1.2
,
design_experiment_3
,
cwd
,
1
,
1
)
assert
single_control
[
'
control_tag_align
'
].
unique
()
==
'
B_1.tagAlign.gz
'
@pytest.mark.singleend
...
...
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