예제 #1
0
        opts.trim[0] = int(opts.trim[0])
        
    if opts.trim[1] == 'None':
        opts.trim[1] = None
    else:
        opts.trim[1] = int(opts.trim[1])





optionsObj = {'kmerSize':opts.ksize,'kmerRange':opts.krange} # need to change the use of this to be how mortals think of numbers
posArgs    = [opts.fasta,opts.regs]
outFile    = opts.out

tWrap = TamoWrap(optionsObj,posArgs)

shorties = 0
if opts.trim:
    for i in tWrap.allSeqs.probes:
        oLen = len(tWrap.allSeqs.probes[i])
        tWrap.allSeqs.probes[i] = tWrap.allSeqs.probes[i][opts.trim[0]:opts.trim[1]]
        nLen = len(tWrap.allSeqs.probes[i])
        #print 'old:%s, new:%s' % (oLen,nLen)
        if not nLen < oLen:
            shorties+=1
if shorties/float(len(tWrap.allSeqs.probes)) > 0.25:
    warn("""WARNING: more than 1/4 of the total sequences were shorter or equal to the length of the requested substring.""")
tWrap.linkedSeqs_seqs = tWrap.allSeqs.seqs_from_ids(tWrap.linkedSeqs_ids)
tWrap.go()
예제 #2
0

# TamoWrap -> def __init__(self, optionsObj, posArgs):

# get list of file paths
dirPath = '/Users/biggus/Documents/James/Data/ReClustering/kmedsPear33Clus50x_2/Clus2_247genes.6EucClus/'
files   = glob.glob('%s*.genes.txt' % (dirPath))

for genesFile in files:
    optionsObj = {'kmerSize':7,'kmerRange':'6,9'} # need to change the use of this to be how mortals think of numbers
    posArgs    = ['/Users/biggus/Documents/James/Data/2KB/2kb_Sequence/2kb_Anopheles/2KBupTSS_goodAffyAGAPsFastasOUT.masked.nr.fas',
                  genesFile]
    
    outFile    = genesFile.replace('.txt','.6-9mers.txt')

    tWrap = TamoWrap(optionsObj,posArgs)
    tWrap.go()
    
    #for l in tWrap.toFile:
        #print l.strip()
    
    print 'num of keepers = %s' % (len(tWrap.output))
    
    outFile = open(outFile, 'w')
    outFile.writelines(tWrap.toFile)
    outFile.close()
    del(outFile)
    
	
	
print 'Done.'