reducing the scope of cli.py to work only after bedtools

sequence_extractor/cli.py

@@ -9,20 +9,18 @@ parser = argparse.ArgumentParser(
     prog = 'transcript_sequence_extractor',
     description = 'extracts transcript sequences from genome sequence and ouputs transcripts with PolyA tail added to them')
 parser.add_argument('--input_fasta_file',
-                    help='genome fasta file')
-parser.add_argument('--input_gtf',
-                    help='gtf file')
+                    help='fasta file obtained from bedtools')
 parser.add_argument('--output_file_name',
-                    help='output fasta file')
+                    help='Name of the output fasta file')
 
 args = parser.parse_args()
 
 def main():
     LOG.info("sequence_extractor begins")
-    exon_extraction_from_gtf()
-    fasta_list = exon_concatenation(args.)
+    fasta_list = exon_concatenation(args.input_fasta_file)
     final_list = poly_a_addition_to_fasta_list(fasta_list)
-    list_to_file(final_list,args.output_file_name)
+    with open(args.output_file_name, 'w') as fasta_out:
+        fasta_out.write('\n'.join('%s\n%s' % x for x in final_list))
     LOG.info("sequence_extractor ends")
 
 if ___name__ == 'main':