diff SAINT_preprocessing.py @ 14:c22c1209e65f draft

Uploaded

--- a/SAINT_preprocessing.py	Tue Apr 12 14:40:42 2016 -0400
+++ b/SAINT_preprocessing.py	Tue Apr 12 14:55:25 2016 -0400
@@ -57,19 +57,7 @@
         for input_line in read_infile:
             input_line = input_line.strip()
             temp = input_line.split('\t')
-            if "Accession Number" in str(temp):
-                if baits[i] in temp:                    
-                    number_bait = temp.index(str(baits[i]))
-                    number_bait = number_bait - 9
-                    bait_cache.append((number_bait, str(bait_line)))
-                    # Locates the Bait names in the column names and then sets the Baits in the 
-                    # correct order in the cache thus the - 9 because the baits start at the 9th
-                    # column.
-                else:
-                    print "Error: bad bait " + str(baits[i])
-                    sys.exit()
-            else:
-                pass
+            bait_cache.append((number_bait, str(bait_line)))
         i = i + 3
 
     bait_cache.sort()
@@ -213,7 +201,7 @@
                 elif "_MOUSE" in prot_id:
                     proteins.append(prot_id)
                 else:
-                    print "Accession must be uniprot ID or gene name"
+                    print "Accession must be uniprot ID or gene"
     return ReturnValue2(data, proteins, header)