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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def _do_subread_set(flag,input_file,of,negative_filter,aligned):
 best = {} cmd = 'samtools view '+flag+' '+input_file sys.stderr.write(cmd+"\n") p = Popen(cmd.split(),stdout=PIPE) z = 0 for line in p.stdout: z += 1 if z%10000==0: sys.stderr.write(str(z) + " subread alignment paths scanned for alignment length\r") pbname = PacBioReadName(_nameprog.match(line).group(1)) mol = pbname.get_molecule() if mol in negative_filter: continue name = pbname.name() sam = SAM(line) c = 0 # aligned base count if we are aligned, subread length if we are not aligned if aligned: c = sam.get_aligned_bases_count() else: c = sam.get_query_length() if mol not in best: best[mol] = [name,c] if c > best[mol][1]: best[mol] = [name,c] p.communicate() sys.stderr.write("\n") sys.stderr.write("Finished analyzing subread lengths\nWriting aligned subreads\n") """After getting all the best alignment counts we can traverse again to keep the best"""

    cmd = 'samtools view '+flag+' '+input_file
    sys.stderr.write(cmd+"\n")
    z = 0
    p = Popen(cmd.split(),stdout=PIPE)
    for line in p.stdout:
      z += 1
      if z%10000==0: sys.stderr.write(str(z) + " subreads alignment paths scanned during selected for best\r")
      pbname = PacBioReadName(_nameprog.match(line).group(1))
      mol = pbname.get_molecule()
      name = pbname.name()
      if mol in negative_filter: continue
      if not best[mol][0] == name: continue
      of.write(line)
    p.communicate()
    for mol in best: negative_filter.add(mol)
    sys.stderr.write("\n")
    sys.stderr.write("molecules written: "+str(len(negative_filter))+"\n")
    return negative_filter