SAM.py 文件源码

def getProperPair(self,outfile=None):
        '''Extract proper paried mapped reads.'''
        if outfile is None:
            outfile = self.fileName + ".PP.sam"
        FO=open(outfile,'w')
        PPcount=0
        print >>sys.stderr, "Writing proper paired reads to\"",outfile,"\"... ",
        for line in self.f:
            hits=[]
            if line[0] == '@':continue                      #skip head lines    
            if ParseSAM._reExpr2.match(line):continue       #skip blank lines
            field=line.rstrip('\n').split() 
            flagCode=string.atoi(field[1])
            if ((flagCode & 0x0001) != 0) and ((flagCode & 0x0002)!=0):
                PPcount +=1
                FO.write(line)
        FO.close()
        print >>sys.stderr, str(PPcount) + " reads were saved!\n",
        self.f.seek(0)