无法输出文件：未创建文件

Question

我是 python 的新手，我很难理解为什么我的程序不会打印，尽管我尽了最大的努力来理解 I/O 和文件处理。

以下代码应采用 fastQ 或 fasta 文件（用于 DNA 或蛋白质序列）并根据用户指定的质量修剪序列，然后使用修剪后的序列创建一个新文件。

当我尝试从命令行运行程序时，问题就来了：

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

程序运行正常（没有错误或跟踪问题），但我没有看到正在创建文件 fQ_out.txt。我认为问题出在 argparse 的某个地方，因为我在运行时没有收到帮助消息：

python endtrim --help

有人可以指点我正确的方向吗？

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 似乎在递归调用自己，而在程序中的任何其他地方根本没有调用它

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()

也许这个选项行应该在main 函数中，还是全局的？