small changes

+ GC content, %changed codons

Author: hoerldavid

optimize.py

@@ -4,6 +4,8 @@
 import sequenceIO
 import kazusaIO
 import optimizing
+import seqstats
+import math
 
 import re
 
@@ -13,15 +15,16 @@ def main(argv):
 
     if (len(argv) != 4):
         print("Usage: optimize.py [sequence file] [source taxid] [target taxid]")
+        sys.exit()
 
     seqfile = argv[1]
     src_taxid = argv[2]
     trg_taxid = argv[3]    
 
     seq = sequenceIO.readFile(seqfile)
     seqr = sequenceIO.D2R(seq)
-    print("== INPUT SEQUENCE:")
-    print(seqr)
+    print("== INPUT SEQUENCE, GC: ", round(seqstats.getGC(seq)*100), "%")
+    print(seq)
 
     cuSrc = kazusaIO.getCU(src_taxid)
     cuTrg = kazusaIO.getCU(trg_taxid)
@@ -32,9 +35,13 @@ def main(argv):
 
     for c in inCodons:
         outCodons.append(opt.optimize(c))
-        
-    print("== OPTIMIZED SEQUENCE:")
-    print("".join(outCodons))
+    
+    res = "".join(outCodons)
+    resd = sequenceIO.R2D(res)
+    print("== OPTIMIZED SEQUENCE, GC: ", round(seqstats.getGC(resd)*100), "%")
+    print(resd)
+    
+    print("== STATS: CHANGED CODONS: ", seqstats.getChanged(seq, resd)[0], "/", seqstats.getChanged(seq, resd)[1])
 
 if __name__ == '__main__':
     main(sys.argv) 

seqstats.py

@@ -0,0 +1,22 @@
+import re
+
+def getGC(seq):
+    gccount = 0;
+    for i in range(0, len(seq)):
+        if (seq[i] == 'G' or seq[i] == 'C'):
+            gccount += 1
+            
+    return float(gccount)/len(seq)
+    
+def getChanged(seq1, seq2):
+    seq1c = re.findall('...', seq1)
+    seq2c = re.findall('...', seq2)    
+    changecount = 0;
+    for i in range(0, len(seq1c)):
+        if (seq1c[i] != seq2c[i]):
+            changecount+=1
+            
+    return (changecount, len(seq1c))
+        
+    
+    

sequenceIO.py

@@ -14,7 +14,7 @@ def readFile(filename):
         ret = parseFASTA(c)
     # else parse raw sequence
     else:
-        ret = parseRAW(c)
+        ret = parseRaw(c)
     return ret