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Fix a bug in lookup #1

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Fix a bug in lookup #1

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36 changes: 17 additions & 19 deletions decode.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -102,7 +102,7 @@ def lookup(seq):
if numrs > 0:
blockId.append(m.group('rnd'))
except:
return []
blockId = []
return blockId


Expand Down Expand Up @@ -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")


Expand All @@ -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
Expand All @@ -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:
Expand All @@ -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,
Expand Down Expand Up @@ -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='"', )

Expand All @@ -320,4 +318,4 @@ def lookup(seq):
row.extend([unique, total, float(unique) / float(total)])
else:
row.extend([0, 0, 0])
csvout.writerow(row)
csvout.writerow(row)