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 createDatabases(targetsFN, wordSize, runName, hasIDs=False):
wordSize = int(wordSize)
hasIDs = (hasIDs == "True")
print 'using IDs', hasIDs
#make sequence list out of targets, make db, write to file
f = open(targetsFN, 'r')
seqList = []
print 'obtaining sequences'
i = 0
for line in f:
if hasIDs:
theID, seq = line.strip().split('\t')
else:
theID, seq = i, line.strip()
seqList.append(cgAlign.cgSeq(theID, seq))
i += 1
f.close()
print 'making word db'
wordDB = cgAlign.createWordDatabase(seqList, wordSize)
cgAlign.writeWordDatabase(wordDB, runName)
print 'making seq db'
seqDB = cgAlign.createSequenceDatabase(seqList)
cgAlign.writeSequenceDatabase(seqDB, runName)
def createDatabases(targetsFN, wordSize, runName, hasIDs = False):
wordSize = int(wordSize)
hasIDs = (hasIDs == "True")
print 'using IDs', hasIDs
#make sequence list out of targets, make db, write to file
f = open(targetsFN, 'r')
seqList = []
print 'obtaining sequences'
i = 0
for line in f:
if hasIDs:
theID, seq = line.strip().split('\t')
else:
theID, seq = i, line.strip()
seqList.append(cgAlign.cgSeq(theID, seq))
i += 1
f.close()
print 'making word db'
wordDB = cgAlign.createWordDatabase(seqList, wordSize)
cgAlign.writeWordDatabase(wordDB, runName)
print 'making seq db'
seqDB = cgAlign.createSequenceDatabase(seqList)
cgAlign.writeSequenceDatabase(seqDB, runName)
def createDatabases(targetsFN, wordSize, runName):
wordSize = int(wordSize)
# make sequence list out of targets, make db, write to file
f = open(targetsFN, "r")
seqList = []
print "obtaining sequences"
i = 0
for line in f:
seqList.append(cgAlign.cgSeq(i, line.strip()))
i += 1
f.close()
print "making word db"
wordDB = cgAlign.createWordDatabase(seqList, wordSize)
cgAlign.writeWordDatabase(wordDB, runName)
print "making seq db"
seqDB = cgAlign.createSequenceDatabase(seqList)
cgAlign.writeSequenceDatabase(seqDB, runName)
def createDatabases(targetsFN, wordSize, runName):
wordSize = int(wordSize)
#make sequence list out of targets, make db, write to file
f = open(targetsFN, 'r')
seqList = []
print 'obtaining sequences'
i = 0
for line in f:
seqList.append(cgAlign.cgSeq(i, line.strip()))
i += 1
f.close()
print 'making word db'
wordDB = cgAlign.createWordDatabase(seqList, wordSize)
cgAlign.writeWordDatabase(wordDB, runName)
print 'making seq db'
seqDB = cgAlign.createSequenceDatabase(seqList)
cgAlign.writeSequenceDatabase(seqDB, runName)
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)
