added script that renames ecoli molecule graph for evaluate.py

deconvolution/main/ecoli_to_interval_renamer.py

+import sys
+if len(sys.argv) < 3:
+    print("renames nodes of a simulated molecule graph into consecutive integers (for evaluate.py)")
+    exit("usage: input output")
+out = open(sys.argv[2],'w')
+for line in open(sys.argv[1]):
+    # change all occurrences of 
+    # xxxxNC_000913.3_100644_115643_0:0:0_0:0:0_14f1/1xxxx
+    # to:
+    # xxxx100644xxxx
+    while "NC_000913" in line:
+        s = line.split("NC_000913")
+        before = s[0] #we'll keep that
+        cur = s[1]    #we'll modify that
+        if len(s) > 2:#we'll keep that too
+            after = "NC_000913" + 'NC_000913'.join(s[2:])
+        else:
+            after = ""
+        #print("before:",before+cur+after)
+        # now we modify 'cur' which hopefully corresponds to [NC_00913].3_100644_115643_0:0:0_0:0:0_14f1/1....[the next NC_00913]
+        s = cur.split('_')
+        val = s[1]    # this is the start coordinate of the molecule, save it
+        cur = '_'.join(s[2:]) # restore the rest of cur
+        s = cur.split('/')
+        rest = '/'.join(s[1:]) # skip until the next '/' char
+        rest = rest[1:]
+        cur = val+rest
+        #print("after:",before+cur+after)
+        line = before + cur + after
+    out.write(line)
+out.close()