SAM.py 文件源码

def getUniqMapRead(self,outfile=None):
        '''Extract uniquely mapped reads.'''
        if outfile is None:
            outfile = self.fileName + ".uniq.sam"
        FO=open(outfile,'w')
        Uniqcount=0
        print >>sys.stderr, "Writing uniquely mapped 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 & 0x0004) == 1: 
                continue            #skip unmapped reads
            #else:
                #print >>sys.stderr,line,
            if (ParseSAM._uniqueHit_pat.search(line)):
                print >>sys.stderr,line,
                Uniqcount +=1
                FO.write(line)
        FO.close()
        print >>sys.stderr, str(Uniqcount) + " reads were saved!\n",
        self.f.seek(0)