Fix the python erros.

workflow/scripts/call_peaks_macs.py

@@ -250,7 +250,6 @@ def main():
     chrom_size = args.size
     paired = args.paired
 
-
     # Create a file handler
     handler = logging.FileHandler('call_peaks.log')
     logger.addHandler(handler)

workflow/scripts/pool_and_psuedoreplicate.py

@@ -192,13 +192,13 @@ def main():
         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[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[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, 'xcor'] = 'Calculate'
 
         # Make 2 self psuedoreplicates
         self_pseudoreplicates_dict = {}

workflow/scripts/utils.py

@@ -85,7 +85,6 @@ def count_lines(filename):
 
 
 def rescale_scores(filename, scores_col, new_min=10, new_max=1000):
-    n_peaks = count_lines(filename)
     sorted_fn = 'sorted-%s' % (filename)
     rescaled_fn = 'rescaled-%s' % (filename)