Refactor code to have consistent use of arguments and referenceing pandas.

workflow/scripts/check_design.py

@@ -21,7 +21,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
-    
+
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -137,23 +137,26 @@ def check_files(design, fastq, paired):
 
 def main():
     args = get_args()
+    design = args.design
+    fastq = args.fastq
+    paired = args.paired
 
     # Create a file handler
     handler = logging.FileHandler('design.log')
     logger.addHandler(handler)
 
-    # Read files
-    design_file = pd.read_csv(args.design, sep='\t')
-    fastq_file = pd.read_csv(args.fastq, sep='\t', names=['name', 'path'])
+    # Read files as dataframes
+    design_df = pd.read_csv(args.design, sep='\t')
+    fastq_df = pd.read_csv(args.fastq, sep='\t', names=['name', 'path'])
 
     # Check design file
-    check_design_headers(design_file, args.paired)
-    check_controls(design_file)
-    check_replicates(design_file)
-    new_design = check_files(design_file, fastq_file, args.paired)
+    check_design_headers(design_df, paired)
+    check_controls(design_df)
+    check_replicates(design_df)
+    new_design_df = check_files(design_file, fastq_df, paired)
 
     # Write out new design file
-    new_design.to_csv('design.tsv', header=True, sep='\t', index=False)
+    new_design_df.to_csv('design.tsv', header=True, sep='\t', index=False)
 
 
 if __name__ == '__main__':

workflow/scripts/experiment_design.py

@@ -21,7 +21,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
-    
+
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -64,19 +64,20 @@ def make_experiment_design(design):
 
 def main():
     args = get_args()
+    design = args.design
 
     # Create a file handler
     handler = logging.FileHandler('experiment_generation.log')
     logger.addHandler(handler)
 
-    # Read files
-    design_file = pd.read_csv(args.design, sep='\t')
+    # Read files as dataframes
+    design_df = pd.read_csv(design, sep='\t')
 
     # Update design file for check_controls
-    new_design = update_controls(design_file)
+    new_design_df = update_controls(design_df)
 
     # write out experiment design files
-    make_experiment_design(new_design)
+    make_experiment_design(new_design_df)
 
 
 if __name__ == '__main__':

workflow/scripts/experiment_qc.py

@@ -25,7 +25,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
-    
+
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -146,6 +146,7 @@ def check_enrichment(sample_id, control_id, sample_reads, control_reads):
 
 def main():
     args = get_args()
+    design = args.design
 
     # Create a file handler
     handler = logging.FileHandler('experiment_qc.log')
@@ -155,18 +156,18 @@ def main():
     check_tools()
 
     # Read files
-    design_file = pd.read_csv(args.design, sep='\t')
+    design_df = pd.read_csv(design, sep='\t')
 
     # Run correlation
-    mbs_filename = generate_read_summary(design_file)
+    mbs_filename = generate_read_summary(design_df)
     check_correlation(mbs_filename)
 
     # Run coverage
-    check_coverage(design_file)
+    check_coverage(design_df)
 
     # Run enrichment
-    new_design = update_controls(design_file)
-    for index, row in new_design.iterrows():
+    new_design_df = update_controls(design_df)
+    for index, row in new_design_df.iterrows():
         check_enrichment(
                             row['sample_id'],
                             row['control_id'],

workflow/scripts/trim_reads.py

@@ -22,7 +22,7 @@ logger.setLevel(logging.INFO)
 
 def get_args():
     '''Define arguments.'''
-    
+
     parser = argparse.ArgumentParser(
         description=__doc__, epilog=EPILOG,
         formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -81,6 +81,8 @@ def trim_reads(fastq, paired):
 
 def main():
     args = get_args()
+    fastq = args.fastq
+    paired = args.paired
 
     # Create a file handler
     handler = logging.FileHandler('trim.log')
@@ -90,7 +92,7 @@ def main():
     check_tools()
 
     # Run trim_reads
-    trim_reads(args.fastq, args.paired)
+    trim_reads(fastq, paired)
 
 
 if __name__ == '__main__':