Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
C
chipseq_analysis
Manage
Activity
Members
Labels
Plan
Issues
19
Issue boards
Milestones
Iterations
Requirements
Code
Merge requests
3
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Locked files
Build
Pipelines
Jobs
Pipeline schedules
Test cases
Artifacts
Deploy
Releases
Container Registry
Operate
Environments
Monitor
Incidents
Service Desk
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Code review analytics
Issue analytics
Insights
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
BICF
Astrocyte
chipseq_analysis
Commits
096e1e79
Commit
096e1e79
authored
5 years ago
by
Venkat Malladi
Browse files
Options
Downloads
Patches
Plain Diff
Fix logic if paired-end and single replicate.
parent
526cd489
Branches
Branches containing commit
Tags
Tags containing commit
1 merge request
!63
Resolve "Single Rep Pool and Pseudo"
Pipeline
#5822
passed with stages
in 14 hours, 57 minutes, and 46 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
workflow/scripts/pool_and_psuedoreplicate.py
+8
-4
8 additions, 4 deletions
workflow/scripts/pool_and_psuedoreplicate.py
with
8 additions
and
4 deletions
workflow/scripts/pool_and_psuedoreplicate.py
+
8
−
4
View file @
096e1e79
...
...
@@ -204,6 +204,7 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
pool_control_tmp
=
bedpe_to_tagalign
(
pool_control
,
"
pool_control
"
)
pool_control
=
pool_control_tmp
# Duplicate rows and update for pool and psuedoreplicates and update tagAlign with single end data
experiment_id
=
design_df
.
at
[
0
,
'
experiment_id
'
]
replicate_files
=
design_df
.
tag_align
.
unique
()
...
...
@@ -237,9 +238,9 @@ 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
# 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
:
...
...
@@ -267,7 +268,10 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
path_to_control
else
:
path_to_pool_control
=
pool_control
if
paired
:
path_to_pool_control
=
cwd
+
'
/
'
+
pool_control
else
:
path_to_pool_control
=
pool_control
design_new_df
[
'
control_tag_align
'
]
=
path_to_pool_control
# Add in pseudo replicates
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment