SAM.py 文件源码

def collapseSAM(self, outfile=None,collevel=10):
        '''At most collevel[default=10] identical reads will be retained in outputting SAM file
        The original SAM file must be sorted before hand. if not, using linux command like "sort -k3,3 -k4,4n myfile.sam >myfile.sorted.sam" '''
        if outfile is None:
            outfile = self.fileName + ".collapsed.sam"
        print >>sys.stderr, "Writing collapsed SAM file to\"",outfile,"\"... "
        FO=open(outfile,'w')        
        flag=""
        for line in self.f:
            if line[0] == '@':continue                      #skip head lines    
            if ParseSAM._reExpr2.match(line):continue       #skip blank lines   
            field=line.rstrip('\n').split() 
            if (string.atoi(field[1]) & 0x0004)!=0: continue    #skip unmapped line 
            id=field[2] + field[3] + field[5]
            if (id != flag):
                FO.write(line)
                flag=id
                skipTrigger=0
            else:
                skipTrigger+=1
                if skipTrigger < collevel:
                    FO.write(line)
                else:continue
        FO.close()
        self.f.seek(0)