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Commit bf79da87 authored by Jeremy Mathews's avatar Jeremy Mathews
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Fix final section indentation

parent f6b5c87b
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1 merge request!54Resolve "Single control or experiment fails at call peaks macs"
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...@@ -229,14 +229,14 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con ...@@ -229,14 +229,14 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
design_new_df.at[3, 'tag_align'] = design_new_df.at[0, 'tag_align'] design_new_df.at[3, 'tag_align'] = design_new_df.at[0, 'tag_align']
# Make 2 self psuedoreplicates # Make 2 self psuedoreplicates
pool_pseudoreplicates_dict = {} self_pseudoreplicates_dict = {}
for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']): for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
replicate_prefix = experiment_id + '_' + str(rep) replicate_prefix = experiment_id + '_' + str(rep)
pool_pseudoreplicates_dict = \ self_pseudoreplicates_dict = \
self_psuedoreplication(tag_file, replicate_prefix, paired) self_psuedoreplication(tag_file, replicate_prefix, paired)
# Update design to include new self pseudo replicates # Update design to include new self pseudo replicates
for rep, pseudorep_file in pool_pseudoreplicates_dict.items(): for rep, pseudorep_file in self_pseudoreplicates_dict.items():
path_to_file = cwd + '/' + pseudorep_file path_to_file = cwd + '/' + pseudorep_file
replicate = rep + 1 replicate = rep + 1
design_new_df.loc[replicate, 'tag_align'] = path_to_file design_new_df.loc[replicate, 'tag_align'] = path_to_file
...@@ -312,25 +312,25 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con ...@@ -312,25 +312,25 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
path_to_pool_control = cwd + '/' + pool_control path_to_pool_control = cwd + '/' + pool_control
design_new_df['control_tag_align'] = path_to_pool_control design_new_df['control_tag_align'] = path_to_pool_control
# Add in pseudo replicates # Add in pseudo replicates
tmp_metadata = design_new_df.loc[0].copy() tmp_metadata = design_new_df.loc[0].copy()
tmp_metadata['control_tag_align'] = path_to_pool_control tmp_metadata['control_tag_align'] = path_to_pool_control
for rep, pseudorep_file in pool_pseudoreplicates_dict.items(): for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep) tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep)
tmp_metadata['replicate'] = str(rep) + '_pr' tmp_metadata['replicate'] = str(rep) + '_pr'
tmp_metadata['xcor'] = 'Calculate'
path_to_file = cwd + '/' + pseudorep_file
tmp_metadata['tag_align'] = path_to_file
design_new_df = design_new_df.append(tmp_metadata)
# Add in pool experiment
tmp_metadata['sample_id'] = experiment_id + '_pooled'
tmp_metadata['replicate'] = 'pooled'
tmp_metadata['xcor'] = 'Calculate' tmp_metadata['xcor'] = 'Calculate'
path_to_file = cwd + '/' + pool_experiment_se path_to_file = cwd + '/' + pseudorep_file
tmp_metadata['tag_align'] = path_to_file tmp_metadata['tag_align'] = path_to_file
design_new_df = design_new_df.append(tmp_metadata) design_new_df = design_new_df.append(tmp_metadata)
# Add in pool experiment
tmp_metadata['sample_id'] = experiment_id + '_pooled'
tmp_metadata['replicate'] = 'pooled'
tmp_metadata['xcor'] = 'Calculate'
path_to_file = cwd + '/' + pool_experiment_se
tmp_metadata['tag_align'] = path_to_file
design_new_df = design_new_df.append(tmp_metadata)
return design_new_df return design_new_df
......
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