Final Revision: Remove If-Else Statement (Redundant)

workflow/scripts/pool_and_psuedoreplicate.py

@@ -204,77 +204,32 @@ 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
 
-    if not replicated:
-
-        # 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()
-        pool_experiment = design_df.tag_align.unique()
-
-        # Update tagAlign with single end data
-        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)
-
-        design_new_df['replicate'] = design_new_df['replicate'].astype(str)
-        design_new_df.at[1, 'sample_id'] = experiment_id + '_pr1'
-        design_new_df.at[1, 'replicate'] = '1_pr'
-        design_new_df.at[1, 'xcor'] = 'Calculate'
-        design_new_df.at[2, 'sample_id'] = experiment_id + '_pr2'
-        design_new_df.at[2, 'replicate'] = '2_pr'
-        design_new_df.at[2, 'xcor'] = 'Calculate'
-        design_new_df.at[3, 'sample_id'] = experiment_id + '_pooled'
-        design_new_df.at[3, 'replicate'] = 'pooled'
-        design_new_df.at[3, 'xcor'] = 'Calculate'
-        design_new_df.at[3, 'tag_align'] = design_new_df.at[0, 'tag_align']
-
-        # Make 2 self psuedoreplicates
-        self_pseudoreplicates_dict = {}
-        for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
-            replicate_prefix = experiment_id + '_' + str(rep)
-            self_pseudoreplicates_dict[rep] = self_psuedoreplication(tag_file, replicate_prefix, paired)
-	    
-
-        # Update design to include new self pseudo replicates
-        self_pseudoreplicates_df = pd.DataFrame.from_dict(self_pseudoreplicates_dict)
-        pool_pseudoreplicates_dict = {}
-        for rep, pseudorep_file in self_pseudoreplicates_df.iterrows():
-            path_to_file = cwd + '/' + pseudorep_file
-            replicate = rep + 1
-            design_new_df.loc[replicate, 'tag_align'] = path_to_file
-            pool_pseudoreplicates_dict[replicate] = path_to_file
-
-        # Drop index column
-        design_new_df.drop(labels='index', axis=1, inplace=True)
-
-    else:
-        # Make pool of replicates
-        replicate_files = design_df.tag_align.unique()
-        experiment_id = design_df.at[0, 'experiment_id']
-        pool_experiment = pool(replicate_files, experiment_id + "_pooled", paired)
-
-        # Make self psuedoreplicates equivalent to number of replicates
-        pseudoreplicates_dict = {}
-        for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
-            replicate_prefix = experiment_id + '_' + str(rep)
-            pr_dict = self_psuedoreplication(tag_file, replicate_prefix, paired)
-            pseudoreplicates_dict[rep] = pr_dict
-
-        # Merge self psuedoreplication for each true replicate
-        pseudoreplicates_df = pd.DataFrame.from_dict(pseudoreplicates_dict)
-        pool_pseudoreplicates_dict = {}
-        for index, row in pseudoreplicates_df.iterrows():
-            replicate_id = index + 1
-            pr_filename = experiment_id + ".pr" + str(replicate_id) + '.tagAlign.gz'
-            pool_replicate = pool(row, pr_filename, False)
-            pool_pseudoreplicates_dict[replicate_id] = pool_replicate
-
-        design_new_df = design_df
-        # Update tagAlign with single end data
-        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)
+    # 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()
+    pool_experiment = pool(replicate_files, experiment_id + "_pooled", paired)
+
+    # Make 2 self psuedoreplicates
+    pseudoreplicates_dict = {}
+    for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
+        replicate_prefix = experiment_id + '_' + str(rep)
+        pr_dict = self_psuedoreplication(tag_file, replicate_prefix, paired)
+        pseudoreplicates_dict[rep] = pr_dict
+
+    # Update design to include new self pseudo replicates
+    pseudoreplicates_df = pd.DataFrame.from_dict(pseudoreplicates_dict)
+    pool_pseudoreplicates_dict = {}
+    for index, row in pseudoreplicates_df.iterrows():
+        replicate_id = index + 1
+        pr_filename = experiment_id + ".pr" + str(replicate_id) + '.tagAlign.gz'
+        pool_replicate = pool(row, pr_filename, False)
+        pool_pseudoreplicates_dict[replicate_id] = pool_replicate
+
+    design_new_df = design_df #.loc[np.repeat(design_df.index, 4)].reset_index()
+    # Update tagAlign with single end data
+    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)
 
     # If paired change to single End
     if paired:

workflow/tests/test_pool_and_psuedoreplicate.py

@@ -70,7 +70,6 @@ def test_single_rep(design_experiment_2):
     shutil.copy(test_design_path + 'A_1.tagAlign.gz', cwd)
     shutil.copy(test_design_path + 'B_1.tagAlign.gz', cwd)
     single_rep = pool_and_psuedoreplicate.generate_design('false', 1.2, design_experiment_2, cwd, 1, 1)
-    print(single_rep)
     assert single_rep.shape[0] == 4
 
 @pytest.mark.singleend