def main():
#Get arguments
args = argParse()
print("- ARGS :")
print(args, "\n")
#create indexedReference
print("- REFERENCE :")
reference = Reference()
#check if already indexed
fileName = path.splitext(args.ref)[0]
# retrieve from .gz
if (path.exists(fileName + ".dumped.gz")):
reference.load(fileName)
print("reference loaded from dumped.gz")
#index sequence
else:
sequence = getSequence(args.ref)
reference.createIndex(sequence)
reference.save(fileName)
print("reference indexed and saved")
print("DEBUG", reference.N)
print("Reference : ", "\n", reference.text[:10], "...", "\n")
#open Reads
print("- READS :")
readStream = openReads(args.reads)
readName, readContent = getNextRead(readStream)
print("First read :", readName, readContent)
print("RevCompl :", reverseCompl(readContent), "\n")
#outputStream
outputStream = open(args.out, "w")
#Start the timer
print("- FINDING ALIGNEMENT :")
with Timer() as total_time:
while (readContent != -1):
print(readName, "(processing)")
isRevCompl = False
bestScore, bestPos = getBestSemiGlobalAlg(readContent, reference,
args.k, args.dmax)
bestScoreRev, bestPosRev = getBestSemiGlobalAlg(
reverseCompl(readContent), reference, args.k, args.dmax)
#if the reverse search is better we take it
if (bestScoreRev < bestScore):
bestScore, bestPos = bestScoreRev, bestPosRev
isRevCompl = True
#Found a result
if (bestScore != len(readContent)):
if bestScore <= args.dmax:
appendResults(outputStream, readName, bestPos, isRevCompl,
bestScore) #with tabs
readName, readContent = getNextRead(readStream)
total_time.print('\nIt tooks {} secondes.', 5)
print()
readStream.close()
outputStream.close()
#print out file
print("- RESULTS :")
f = open(args.out, "r")
print(f.read())
f.close()
print("exported in:", args.out)
