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)
