From c0fbe1f8b1ad14a33c59c3e943b7bb018eef0d2e Mon Sep 17 00:00:00 2001
From: hbyang <hbyang@Z840-centos6.9>
Date: Fri, 11 May 2018 14:23:02 +0800
Subject: [PATCH] Fix a bug in lookup

---
 decode.py | 36 +++++++++++++++++-------------------
 1 file changed, 17 insertions(+), 19 deletions(-)

diff --git a/decode.py b/decode.py
index 91b0490..3a542d7 100644
--- a/decode.py
+++ b/decode.py
@@ -62,17 +62,17 @@ def read_building_block_sequence(filename):
         try:
             (seq, mol, cyc) = (col[0], col[1], col[2])
         except:
-            print "[Error] expecting 3 columns for each line: <sequence> <building-block-id> <cycle-number>"
-            print "[Error] line %d: %s" % (linenumber, line)
+            print("[Error] expecting 3 columns for each line: <sequence> <building-block-id> <cycle-number>")
+            print("[Error] line %d: %s" % (linenumber, line))
             sys.exit(1)
 
         if not cyc in mapobj:
             mapobj[cyc] = {}
 
         if seq in mapobj[cyc]:
-            print "[Error] identical sequence already assigned to a building block %s for cycle %s" % (
-                mapobj[cyc][seq], cyc)
-            print "[Error] line %d: %s" % (linenumber, line)
+            print("[Error] identical sequence already assigned to a building block %s for cycle %s" % (
+                mapobj[cyc][seq], cyc))
+            print("[Error] line %d: %s" % (linenumber, line))
             sys.exit(2)
         else:
             mapobj[cyc][seq] = mol
@@ -102,7 +102,7 @@ def lookup(seq):
         if numrs > 0:
             blockId.append(m.group('rnd'))
     except:
-        return []
+        blockId = []
     return blockId
 
 
@@ -152,14 +152,14 @@ def lookup(seq):
 message += "regex= %s\n" % scheme
 message += "number of building blocks= %d\n" % numbb
 message += "number of random seq. blocks= %d\n" % numrs
-print message
+print(message)
 logfile.write(message + "\n")
 
 
 """ read building block sequence info. """
 BBTag = read_building_block_sequence(options.bbseq)
 message = "Reading building blocks from '%s'\n" % options.bbseq
-print message
+print(message)
 logfile.write(message + "\n")
 
 
@@ -171,7 +171,7 @@ def lookup(seq):
     for i in range(1, numbb + 1):
         Count[fileIdx][i]= {}
         CountSum[fileIdx][i]= {}
-        for j in combinations(range(1, numbb + 1), i):
+        for j in combinations(list(range(1, numbb + 1)), i):
             classId= ''.join(map(str, j))
             Count[fileIdx][i][classId]= {}
             CountSum[fileIdx][i][classId]= 0
@@ -194,16 +194,14 @@ def lookup(seq):
             blockId = lookup(raw)
             if not blockId and options.revcomp : # try again
                 blockId = lookup(revcomp(raw))
-                if not blockId:
-                    continue
-            else:
+            if not blockId:
                 continue
 
             success += 1
 
             # store blockId
             for i in range(1, numbb + 1):
-                for j in combinations(range(1, numbb + 1), i):
+                for j in combinations(list(range(1, numbb + 1)), i):
                     classId = ''.join(map(str, j))
                     combiId = []
                     for k in j:
@@ -227,20 +225,20 @@ def lookup(seq):
                 Unique[fileIdx][combiId]['set'] = {randomSeq}
 
     message += "number of seq.= %d (success= %d)\n" % (reading, success)
-    print message
+    print(message)
     logfile.write(message + "\n")
 
 """ write out csv output """
 message = "Writing sequence counts"
-print message
+print(message)
 logfile.write(message + "\n")
 
 for i in range(1, numbb + 1):
-    for j in combinations(range(1, numbb + 1), i):
+    for j in combinations(list(range(1, numbb + 1)), i):
         classId = ''.join(map(str, j))
         filename = options.prefix + '_' + classId + '.csv'
         csvfile = open(filename, 'w')
-        print filename
+        print(filename)
         logfile.write(filename + "\n")
 
         # For a given classId,
@@ -298,7 +296,7 @@ def lookup(seq):
 filename = options.prefix + '_unique.csv'
 csvfile = open(filename, 'w')
 message = "\nWriting sequence uniqueness to '%s'" % filename
-print message
+print(message)
 logfile.write(message + "\n")
 csvout = csv.writer(csvfile, delimiter=',', quotechar='"', )
 
@@ -320,4 +318,4 @@ def lookup(seq):
             row.extend([unique, total, float(unique) / float(total)])
         else:
             row.extend([0, 0, 0])
-    csvout.writerow(row)
\ No newline at end of file
+    csvout.writerow(row)