remove errors from generate_design function

workflow/scripts/pool_and_psuedoreplicate.py

@@ -322,22 +322,6 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
         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'    else:
-        path_to_pool_control = cwd + '/' +  pool_control
-        design_new_df['control_tag_align'] = path_to_pool_control
-
-    # Add in pseudo replicates
-    tmp_metadata = design_new_df.loc[0].copy()
-    tmp_metadata['control_tag_align'] = path_to_pool_control
-    for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
-        tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep)
-        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'
@@ -346,16 +330,6 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
     tmp_metadata['tag_align'] = path_to_file
     design_new_df = design_new_df.append(tmp_metadata)
 
-    # Write out new dataframe
-    design_new_df.to_csv(experiment_id + '_ppr.tsv',
-                         header=True, sep='\t', index=False)
-
-    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
 
 

workflow/tests/test_pool_and_psuedoreplicate.py

@@ -5,7 +5,6 @@ import pandas as pd
 from io import StringIO
 import os
 import pool_and_psuedoreplicate
-import sys
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/design/'