无法输出文件：没有创建文件

Question

我是全新的python，并且很努力地理解为什么我的程序不会打印尽管我尽我所能了解I/O和文件处理。

下面的代码应该采用fastQ或fasta文件（对于DNA或蛋白质序列），并根据用户指定的质量修剪序列，然后用修剪后的序列创建一个新文件。

麻烦的是当我尝试运行命令行程序：

python endtrim --min_q 35 --in_33 fQ.txt --out_33 fQ_out.txt 

程序运行无事故（没有任何错误或追溯的问题），但我没有看到文件fQ_out.txt被创建。依我看，问题在于argparse的地方，因为我没有得到帮助信息中运行时：

python endtrim --help 

可有人请点我在正确的方向？

from __future__ import division, print_function 
import argparse 
import collections 
import sys 
import re 
from string import punctuation 
from fastRead import * 
ready2trim =() 

def parse_arguments(): 
    """Creates a bevvy of possible sort arguments from command line and 
    binds them to their respective names""" 
    parser = argparse.ArgumentParser("--h", "--help", description=__doc__, \ 
            formatter_class=argparse.\ 
            RawDescriptionHelpFormatter) 
    options = parse_arguments() 

    #quality argument 
    parser.add_argument("--min_qual", action='store', default=30, \ 
         dest='min_qual', help="""Lowest quality value 
         that can appear in the output""") 
    #input arguments 
    parser.add_argument("--in_33", action='store', default=sys.stdin, \ 
         dest='in_33', nargs='?', help="""Input file in fastq format, using Phred+33 coding""") 
    parser.add_argument("--in_64", action='store', default=sys.stdin, \ 
         dest='in_64', nargs='?', help="""Input file in fastq format, using Phred+64 coding""") 
    parser.add_argument("--in_fasta", action='store', default=sys.stdin, \ 
         dest='in_fasta', nargs='?', help="""Input fasta format, requires concurrent --in_qual argument""") 
    parser.add_argument("--in_qual", action='store', default=sys.stdin, \ 
         dest='in_qual', nargs='?', help="""Input quality format, requires concurrent --in_fasta argument""")      
    #output arguments 
    parser.add_argument("--out_33", action='store', default=sys.stdout, \ 
         dest='out_33', nargs='?', help="""Output file in fastq format, 
         using Phred+33 coding""") 
    parser.add_argument("--out_64", action='store', default=sys.stdout, \ 
         dest='out_64', nargs='?', help="""Output file in fastq format, 
         using Phred+33 coding""")     
    parser.add_argument("--out_fasta", action='store', default=sys.stdout, \ 
         dest='out_fasta', nargs='?', help="""Output fasta format, 
         """) 
    parser.add_argument("--out_qual", action='store', default=False, \ 
         dest='out_qual', nargs='?', help="""Output quality format, 
         """)  
    args = parser.parse_args() 
    return args 

def incoming(args): 
    """interprets argparse command and assigns appropriate format for 
    incoming file""" 
    if options.in_fasta and options.in_qual: 
     #ready2trim is the input after being read by fastRead.py 
     ready2trim = read_fasta_with_quality(open(options.in_fasta), \ 
     open(options.in_qual)) 
     return ready2trim 
    elif options.in_33: 
     ready2trim = read_fastq(open(options.in_33)) 
     #phredCode_in specifies the Phred coding of the input fastQ 
     phredCode_in = 33 
     return ready2trim 
    elif options.in_64: 
     ready2trim = read_fastq(open(options.in_64)) 
     phredCode_in = 64 
     return ready2trim 
    else: sys.stderr.write("ERR: insufficient input arguments") 

def print_output(seqID, seq, comm, qual): 
    """interprets argparse command and creates appropriate format for 
    outgoing file""" 
    #Printing a fastQ 
    if options.out_33 or options.out_64: 
     if options.out_33: 
      #phredCode_out specifies the Phred coding of the output fastQ 
      phredCode_out = 33 
      if comm: 
       #outputfh is the file handle of new output file 
       with open(options.out_33,'a') as outputfh: 
        outputfh.write("@{}\n{}\n{}\n+".format(seqID, seq, comm)) 
      else: 
       with open(options.out_33,'a') as outputfh: 
        outputfh.write("@{}\n{}\n+".format(seqID, seq))    
     else: 
      phredCode_out = 64 
      if comm: 
       #outputfh is the file handle of new output file 
       with open(options.out_33,'a') as outputfh: 
        outputfh.write("@{}\n{}\n{}\n+".format(seqID, seq, comm)) 
      else: 
       with open(options.out_33,'a') as outputfh: 
        outputfh.write("@{}\n{}\n+".format(seqID, seq)) 
     print(''.join(str(chr(q+phredCode_out)) for q in qual)) 
    #Print a fasta 
    if options.out_fasta: 
     outputfh = open(options.out_fasta, "a") 
     if(comment == ''): 
      output.write('>{}\n{}\n'.format(seqID, seq)) 
     else: output.write('>{} {}\n{}\n'.format(seqID, comm, seq)) 
    #Print a qual 
    if options.out_qual: 
     outputfh = open(options.out_qual, "a") 
     if(comment == ''): 
      output.write('>{}\n{}\n'.format(seqID, seq)) 
     else: output.write('>{} {}\n{}\n'.format(seqID, comm, seq)) 

def main(args): 
    """Prints combined fastq sequence from separate fasta and quality 
    files according to user-generated arguments """ 
    for (seqID, seq, comm, qual) in ready2trim: 
     for q in qual: 
      #i counts satisfactory bases to later print that number of 
      i = 0 
      if ord(q) - phredCode_in >= min_qual: 
       i += 1 
      print_output(seqID, seq[0:i], comm, qual[0:i]) 
     sys.stderr.write("ERR: sys.stdin is without sequence data") 

if __name__ == "__main__" : 
    sys.exit(main(sys.argv)) 

Answer 1

parse_arguments似乎是递归调用本身，而它不是在程序

def parse_arguments(): 
    """Creates a bevvy of possible sort arguments from command line and 
    binds them to their respective names""" 
    parser = argparse.ArgumentParser("--h", "--help", description=__doc__, \ 
            formatter_class=argparse.\ 
            RawDescriptionHelpFormatter) 
    options = parse_arguments() 

也许这选项线应该是在main功能，或者在全球都被称为从其他地方？