Very large input and piping using subprocess.Popen

Question

I have pretty simple problem. I have a large file that goes through three steps, a decoding step using an external program, some processing in python, and then recoding usi

Answer 1

Try to make this small change, see if the efficiency is better.

 for line in samtoolsin.stdout:
        if(line.startswith("@")):
            samtoolsout.stdin.write(line)
        else:
            linesplit = line.split("\t")
            if(linesplit[10]=="*"):
                linesplit[9]="*"
            samtoolsout.stdin.write("\t".join(linesplit))