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chipseq_analysis
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BICF
Astrocyte
chipseq_analysis
Commits
57872294
Commit
57872294
authored
5 years ago
by
Jeremy Mathews
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change design_df
parent
d21683d4
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1 merge request
!54
Resolve "Single control or experiment fails at call peaks macs"
Pipeline
#4527
failed with stages
in 30 seconds
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1
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1 changed file
workflow/scripts/pool_and_psuedoreplicate.py
+4
-4
4 additions, 4 deletions
workflow/scripts/pool_and_psuedoreplicate.py
with
4 additions
and
4 deletions
workflow/scripts/pool_and_psuedoreplicate.py
+
4
−
4
View file @
57872294
...
...
@@ -209,7 +209,7 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
# Duplicate rows and update for pool and psuedoreplicates and update tagAlign with single end data
experiment_id
=
design_df
.
at
[
0
,
'
experiment_id
'
]
replicate
=
design_df
.
at
[
0
,
'
replicate
'
]
design_new_df
=
design_df
.
loc
[
np
.
repeat
(
design_df
.
index
,
4
)].
reset_index
()
design_new_df
=
design_df
#
.loc[np.repeat(design_df.index, 4)].reset_index()
pool_experiment
=
design_df
.
tag_align
.
unique
()
# Update tagAlign with single end data
...
...
@@ -272,9 +272,6 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
if
paired
:
design_new_df
[
'
tag_align
'
]
=
design_new_df
[
'
se_tag_align
'
]
design_new_df
.
drop
(
labels
=
'
se_tag_align
'
,
axis
=
1
,
inplace
=
True
)
# Check controls against cutoff_ratio
# if so replace with pool_control
# unless single control was used
# If paired change to single End
if
paired
:
...
...
@@ -282,6 +279,9 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
else
:
pool_experiment_se
=
pool_experiment
# Check controls against cutoff_ratio
# if so replace with pool_control
# unless single control was used
if
not
single_control
:
path_to_pool_control
=
cwd
+
'
/
'
+
pool_control
if
control_df
.
values
.
max
()
>
cutoff_ratio
:
...
...
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