def alignSeqs(seqsFN, dbName, wordSize, outFN, maxNumMismatches, sendExitSignal = False):
maxNumMismatches = int(maxNumMismatches)
sendExitSignal = bool(sendExitSignal)
timer = bioLibCG.cgTimer()
timer.start()
#put seqs in cgSeq object, align
wName = dbName + '.wDB'
sName = dbName + '.sDB'
wordSize = int(wordSize)
#load dbs
#print 'loading Sequence Database'
sDB = cgAlign.loadSequenceDatabase(sName)
print timer.split()
#print 'loading Word Database'
wDB = cgAlign.loadWordDatabase(wName)
print timer.split()
#align each seq
f = open(seqsFN, 'r')
fOut = open(outFN, 'w')
for line in f:
qSeq = cgAlign.cgSeq(line.strip().split('\t')[0], line.strip().split('\t')[1])
#write out the alignments
cgAlign.alignQuery(qSeq, wDB, sDB, wordSize, maxNumMismatches, fOut)
f.close()
fOut.close()
print timer.split()
if sendExitSignal:
cgExit.sendExitSignal(seqsFN)
def alignSeqs(seqsFN,
dbName,
wordSize,
outFN,
maxNumMismatches,
sendExitSignal=False):
maxNumMismatches = int(maxNumMismatches)
sendExitSignal = bool(sendExitSignal)
timer = bioLibCG.cgTimer()
timer.start()
#put seqs in cgSeq object, align
wName = dbName + '.wDB'
sName = dbName + '.sDB'
wordSize = int(wordSize)
#load dbs
#print 'loading Sequence Database'
sDB = cgAlign.loadSequenceDatabase(sName)
print timer.split()
#print 'loading Word Database'
wDB = cgAlign.loadWordDatabase(wName)
print timer.split()
#align each seq
f = open(seqsFN, 'r')
fOut = open(outFN, 'w')
for line in f:
qSeq = cgAlign.cgSeq(line.strip().split('\t')[0],
line.strip().split('\t')[1])
#write out the alignments
cgAlign.alignQuery(qSeq, wDB, sDB, wordSize, maxNumMismatches, fOut)
f.close()
fOut.close()
print timer.split()
if sendExitSignal:
cgExit.sendExitSignal(seqsFN)
import cgAlign
query = 'CATACTTCCACGCCCAGCTCCATAATAACCC'
#target = 'ATGCGTGTTTCTTGCGCGATCG'
#format the sequences
#tSeq = cgAlign.cgSeq(0,target)
#tSeqList = [tSeq]
qSeq = cgAlign.cgSeq(0, query)
#Make target databases
#seqDB = cgAlign.createSequenceDatabase(tSeqList)
#wordDB = cgAlign.createWordDatabase(tSeqList, 4)
#print tSeqList
#print seqDB
#print wordDB
seqDB = cgAlign.loadSequenceDatabase('tester.sDB')
wordDB = cgAlign.loadWordDatabase('tester.wDB')
cgAlign.alignQuery(qSeq, wordDB, seqDB, 5)
import cgAlign
query = 'CATACTTCCACGCCCAGCTCCATAATAACCC'
#target = 'ATGCGTGTTTCTTGCGCGATCG'
#format the sequences
#tSeq = cgAlign.cgSeq(0,target)
#tSeqList = [tSeq]
qSeq = cgAlign.cgSeq(0, query)
#Make target databases
#seqDB = cgAlign.createSequenceDatabase(tSeqList)
#wordDB = cgAlign.createWordDatabase(tSeqList, 4)
#print tSeqList
#print seqDB
#print wordDB
seqDB = cgAlign.loadSequenceDatabase('tester.sDB')
wordDB = cgAlign.loadWordDatabase('tester.wDB')
cgAlign.alignQuery(qSeq, wordDB, seqDB, 5)
