Exemplo n.º 1
0
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)
Exemplo n.º 2
0
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)
Exemplo n.º 3
0
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)
Exemplo n.º 4
0
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)