Exemplo n.º 1
0
def  Write_SeqFile(seq,id) :
    masked_seq= Pick70_mask.mask_longAT(seq,"lower")
    outfile = '~temp' + string.replace(id[:100],'/','')
    out = open(outfile, 'w')
    out.write('>'+id+'\n')
    out.write(masked_seq +'\n') 
    out.close()
    return outfile
Exemplo n.º 2
0
def filter_mask(data_dic, SYMBOL_LIST, TOLERANT, MASK):
    new_dic = {}
    for key in data_dic.keys():
        seq = data_dic[key][4]
        os.environ["seq"] = seq
        mask = Pick70_mask.mask(seq, SYMBOL_LIST, TOLERANT)
        if mask <= MASK:
            new_dic[key] = data_dic[key][:]
    print "mask:", len(data_dic.keys()), len(new_dic.keys())
    return new_dic
Exemplo n.º 3
0
        if (os.access(genome+".nsq", os.R_OK)) and (os.access(genome+".nin", os.R_OK)) and (os.access(genome+".nhr", os.R_OK)):
            pass
        else:
            fr, fw, fe = os.popen3('formatdb -i $genome -p F')
            errormessage = fe.read()
            fr.close()
            fw.close()
            fe.close()
            if errormessage!="":
                print errormessage
                print "program terminated"
                sys.exit(1)

        maskinput =open('~maskedinput','w')
        for id in index:
            masked_seq = Pick70_mask.mask_longAT(seq_dic[id],"lower")
            maskinput.write('>'+id+'\n')
            maskinput.write(masked_seq+'\n')
        maskinput.close()

        os.environ['input'] = '~maskedinput'
        fr, fw, fe = os.popen3('blastall -i "$input" -d $genome -a $cpunum -p blastn -v 50 -b 50 -e 1  -o ~tempblatout  -F "m D" -U')

    elif (VERSION =="BLAT"):
        Pick70_mask.mask_file(tempinput,input+".mask","dust", "lower")
        #blat version
        fr,fw,fe  = os.popen3('blat "$genome" "$input".mask -out=blast -qMask=lower ~tempblatout')
        
    elif (VERSION =="GFCLIENT"):
        Pick70_mask.mask_file(tempinput,input+".mask","dust", "lower")
        #gfCleint version