Python alignQuery Exemples

Exemple #1

Fichier : alignSeqs.py Projet : JasonAng/ResearchScripts

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)

Exemple #2

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)

Exemple #3

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)

Exemple #4

Fichier : CONTROL.py Projet : JasonAng/ResearchScripts

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)