--- a/Protein_report_processing.py	Tue Aug 23 19:18:49 2016 -0400
+++ b/Protein_report_processing.py	Tue Aug 23 19:21:40 2016 -0400
@@ -9,14 +9,20 @@
 # still need a way to match files to bait identifiers
 # or they can just be required to be put in the order of the bait file
 quant_type = sys.argv[3] # what metric to use for quantification
+print quant_type
 # "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs"
 db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker
+print db
 prey = sys.argv[5]
+print prey
 tool_path = sys.argv[7]
+print tool_path
 if db == "None":
     db = str(tool_path)  + "/SwissProt_HUMAN_2015_12.fasta"
 make_bait = sys.argv[6]
+print make_bait
 bait_bool = sys.argv[8]
+print bait_bool
 
 def bait_create(baits, infile):
     # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
@@ -134,7 +140,7 @@
         genename = 'NA'
         return ReturnValue1(seqlength, genename)
 def concatenate_files(file_list_string, bait_file):
-    file_list = file_list_string.split(", ")
+    file_list = file_list_string.split(",")
     bait = read_tab(bait_file)
     master_table = []
     header_check = 0