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Commit 096e1e79 authored by Venkat Malladi's avatar Venkat Malladi
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Fix logic if paired-end and single replicate.

parent 526cd489
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1 merge request!63Resolve "Single Rep Pool and Pseudo"
Pipeline #5822 passed with stages
in 14 hours, 57 minutes, and 46 seconds
......@@ -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
......
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