added -interm option

bayespairing/src/parse_sequences.py

@@ -116,6 +116,11 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
     else:
         o = "output"
 
+    if "interm" in arguments:
+         interm = True
+    else:
+         interm = False
+		
     if "sscons" in arguments:
         sscons = arguments["sscons"]
     else:
@@ -136,6 +141,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                 if len(seq) <= 200:
                     #print("Running BayesPairing on full sequence")
                     maxs = run_BP(seq, ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k)
+                    if interm:
+                        print('PURE SEQUENCE RESULTS:',maxs)
                     all_maxes = []
                     for ind, mod in enumerate(modules_to_parse):
                         all_maxes.append([mod, *maxs[ind]])
@@ -148,6 +155,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                         #print("Running BayesPairing on sequence window:", index, index + w)
                         bf = max(0, index)
                         maxs = run_BP(seq[index:index + w], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k)
+                        if interm:
+                            print('PURE SEQUENCE RESULTS:',maxs)
                         for mod in modules_to_parse:
                             corrected_maxes = []
                             for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
@@ -159,6 +168,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                         index = index + s
                     #print("Running BayesPairing on sequence window:", index, len(seq))
                     maxs = run_BP(seq[index:], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k)
+                    if interm:
+                        print('PURE SEQUENCE RESULTS:',maxs)
                     for mod in modules_to_parse:
                         corrected_maxes = []
                         for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
@@ -193,6 +204,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                 if len(seq) <= 200:
                     #print("Running BayesPairing on full sequence")
                     maxs = run_BP(seq, ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
+                    if interm:
+                        print('PURE SEQUENCE RESULTS:',maxs)
                     all_maxes = []
                     for ind, mod in enumerate(modules_to_parse):
                         all_maxes.append([mod, *maxs[ind]])
@@ -205,6 +218,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                         #print("Running BayesPairing on sequence window:", index, index + w)
                         bf = max(0, index)
                         maxs = run_BP(seq[index:index + w], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
+                        if interm:
+                            print('PURE SEQUENCE RESULTS:',maxs)
                         for mod in modules_to_parse:
                             corrected_maxes = []
                             for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
@@ -216,6 +231,8 @@ def run_fasta(input, modules_to_parse, dataset, ss="", arguments={}):
                         index = index + s
                     #print("Running BayesPairing on sequence window:", index, len(seq))
                     maxs = run_BP(seq[index:], ss, modules_to_parse, dataset, "NONE", m, n, sm, mc, p, k,sscons)
+                    if interm:
+                        print('PURE SEQUENCE RESULTS:',maxs)
                     for mod in modules_to_parse:
                         corrected_maxes = []
                         for ind, cand in enumerate(maxs[modules_to_parse.index(mod)]):
@@ -358,6 +375,7 @@ if __name__ == "__main__":
     parser.add_argument("-s", help="Step size between windows [10 to 200]. Default:100 ")
     parser.add_argument("-sw", help="weight of the secondary structure analysis [0.8 to 2]. Default:1 ")
     parser.add_argument("-o", help="Name of the output file. Default: output ")
+    parser.add_argument("-interm", help="output the best intermediate results. (use -interm 1)")
     parser.add_argument("-sscons", help="Constraint level of the module-secondary structure match. Integer from 0 to 5, 0 being most constrained")
 
     args = parser.parse_args()
@@ -387,6 +405,8 @@ if __name__ == "__main__":
         arguments["sscons"] = args.sscons
     if args.mod != None:
         arguments["mod"] = args.mod
+    if args.interm != None:
+        arguments["interm"] = args.mod
     if args.seq != None:
         seq = args.seq
     else: