Resolve "Run File Helper Script"

Closes #11 (closed) Created the script to generate a run file from a list of experiments. Fixed a few minor bugs while testing the runs as well.

chipathlon/jobs/scripts/db_save_result.py

@@ -18,14 +18,15 @@ if os.path.isfile(args.file) and os.path.isfile(args.meta):
         meta = yaml.load(rh)
     valid = False
     msg = ""
+
     if meta["result_type"] == "bed":
-        valid, msg, data = mdb.save_bed(args.file, meta["control_sample_ids"], meta["experiment_sample_ids"], meta)
+        valid, msg, data = mdb.save_bed(args.file, meta["control_sample_accessions"], meta["signal_sample_accessions"], meta)
     elif meta["result_type"] == "peak":
-        valid, msg, data = mdb.save_peak(args.file, meta["control_sample_ids"], meta["experiment_sample_ids"], meta)
-    elif meta["result_type"] == 'bam':
-        valid,msg,data = mdb.save_bam(args.file, meta["control_sample_ids"], meta["experiment_sample_ids"], meta)
+        valid, msg, data = mdb.save_peak(args.file, meta["control_sample_accessions"], meta["signal_sample_accessions"], meta)
+    elif meta["result_type"] == "bam":
+        valid, msg, data = mdb.save_bam(args.file, meta["control_sample_accessions"], meta["signal_sample_accessions"], meta)
+
+    print msg
 
-    print msg 
-        
 else:
     print "Either input file %s or meta file %s does not exist." % (args.file, args.meta)