add helper_function to convert geneCluster.json into csv

scripts/helper_functions.py

@@ -0,0 +1,24 @@
+import os, json
+import argparse
+
+parser = argparse.ArgumentParser(description='convert geneCluster.json into a csv file ',\
+         usage=' python %(prog)s'+'  -in /path/geneCluster.json -out /path/geneCluster_stats.csv')
+parser.add_argument('-in',  '--input_filepath',  type = str, required=True, help='')
+parser.add_argument('-out', '--output_filepath', type = str, required=True, help='')
+params = parser.parse_args()
+input_filepath=params.input_filepath
+output_filepath=params.output_filepath
+
+def convert_cluster_statistics_csv(input_path, output_path):
+    with open(input_path) as inputf,\
+         open(output_path, 'w') as outputf:
+        cluster_stats_list= json.load(inputf)
+        header_list=['count','ann','dupli','GName','geneLen','event','msa','divers','geneId','allAnn','dup_detail','allGName','locus']
+        header_description=['#strain count','major annotation','whether duplicated','major gene name','gene length','number of gene events','clusterID','diversity','gene ID','all annotations','duplication details','all gene names','all locus tags']
+        outputf.write(','.join([ header for header in header_description ]))
+        outputf.write('\n')
+        for cluster_stats in cluster_stats_list:
+            outputf.write(','.join([ str(cluster_stats[header]) for header in header_list ]))
+            outputf.write('\n')
+
+convert_cluster_statistics_csv(input_filepath, output_filepath)