# HG changeset patch
# User bornea
# Date 1447958311 18000
# Node ID 729aac64ce430787a8ba900681d2c25511d05c83
# Parent  9e0a894d26761ff6a6f68a534368ddfbf3a646dc
Uploaded

diff -r 9e0a894d2676 -r 729aac64ce43 SAINT_preprocessing_v6_mq_pep.py
--- a/SAINT_preprocessing_v6_mq_pep.py	Thu Nov 19 13:38:20 2015 -0500
+++ b/SAINT_preprocessing_v6_mq_pep.py	Thu Nov 19 13:38:31 2015 -0500
@@ -17,14 +17,16 @@
 # 3) prey: Y or N for generating a prey file (requires internet connection)
 #######################################################################################
 mq_file = sys.argv[1]
-cmd = r"Rscript /home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/pre_process_protein_name_set.R " + str(mq_file) 
+ins_path = sys.argv[8]
+names_path = str(ins_path) + r"uniprot_names.txt"
+cmd = r"Rscript "+ str(ins_path) +"pre_process_protein_name_set.R " + str(mq_file) + " " + str(names_path)
 os.system(cmd)
 
 infile = "./tukeys_output.txt" #maxquant "Samples Report" output
 prey = sys.argv[2] # Y or N
 fasta_db = sys.argv[3]
 if fasta_db == "None":
-    fasta_db = "/home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/SwissProt_HUMAN_2014_08.fasta"
+    fasta_db = str(ins_path)  + "SwissProt_HUMAN_2014_08.fasta"
 make_bait= sys.argv[6]
 
 def bait_create(baits, infile):