Fixed function calls with providing correct parameters 2.

samplesheet_generator.py

@@ -163,7 +163,7 @@ def paired_i7_index_id_index(i7_index_id, index, indexes):
 
 # TODO: the following function should be rewriten and broken down to smaller functions so that it is easier to read and understand what's going on
 
-def print_data_section_v1(dual_indexes, index_length, indexes, input_info_file):
+def print_data_section_v1(run_id, dual_indexes, index_length, indexes, input_info_file):
 
 	info_df = pd.read_csv(input_info_file, sep='\t', comment='#', header=0)
 	info_df = info_df.fillna('')
@@ -176,7 +176,7 @@ def print_data_section_v1(dual_indexes, index_length, indexes, input_info_file):
 
 		for index, row in info_df.iterrows():
 
-			if (str(row['run_id']) == args.run_id):
+			if (str(row['run_id']) == run_id):
 			# select only samples from a run with the given run_id
 
 				sample_id = row['sample_id']
@@ -265,7 +265,7 @@ def print_data_section_v1(dual_indexes, index_length, indexes, input_info_file):
 
 		for index, row in info_df.iterrows():
 
-			if (str(row['run_id']) == args.run_id):
+			if (str(row['run_id']) == run_id):
 			# select only samples from a run with the given run_id
 
 				sample_id = row['sample_id']
@@ -389,6 +389,8 @@ def main():
 
 	args=parser.parse_args()
 
+	run_id                      = args.run_id
+	index_type                  = args.index_type
 	index_length                = args.index_length
 	investigator_name           = args.investigator_name
 	experiment_name             = args.experiment_name
@@ -407,17 +409,17 @@ def main():
 	# check whether the specified set of indexes is supported
 	# if so then load them into indexes
 
-	if   (args.index_type.lower() == "dual"):
+	if   (index_type.lower() == "dual"):
 		dual_indexes = True
-	elif (args.index_type.lower() == "simple"):
+	elif (index_type.lower() == "simple"):
 		dual_indexes = False
 	else:
 		sys.exit("Unsupported value of index_type=\'"+args.index_type+"\' provided.")	
 
-	if not (args.index_length == 8) and not (args.index_length == 10):
-		sys.exit("Unsupported value of index_length=\'"+args.index_length+"\' provided.")
-	elif not dual_indexes and (args.index_length == 10):
-		sys.exit("Unsupported value of index_length=\'"+args.index_length+"\' for simple indexes provided.")
+	if not (index_length == 8) and not (index_length == 10):
+		sys.exit("Unsupported value of index_length=\'"+index_length+"\' provided.")
+	elif not dual_indexes and (index_length == 10):
+		sys.exit("Unsupported value of index_length=\'"+index_length+"\' for simple indexes provided.")
 
 	indexes=assign_indexes(dual_indexes, index_length)
 
@@ -429,7 +431,7 @@ def main():
 		print_header_section_v1(investigator_name, experiment_name)
 		print_reads_section_v1(read_length_1, read_length_2)
 		print_settings_section_v1(adapter_read_1, adapter_read_2, adapter_behavior, minimum_trimmed_read_length, mask_short_reads, override_cycles)
-		print_data_section_v1(dual_indexes, index_length, indexes, input_info_file)
+		print_data_section_v1(run_id, dual_indexes, index_length, indexes, input_info_file)
 	elif (samplesheet_version == 'v2'):
 		sys.exit("Not implemented yet")
 	else: