Python代码将stdin和stdout重定向到Shell脚本

Question

I am trying to write a program that reads from a file and writes to a new file using the command line. I am using the CommandLine class and using ArgParse to accept different args as well as the file names for input and output. I am trying to redirect stdin and stdout to these files. However, I keep getting an error that I put at the bottom of the code below. Am I inputting the arguments to the command line incorrectly, or is something else going on? All of my files are in the same folder.

class CommandLine() :
'''
Handle the command line, usage and help requests.

CommandLine uses argparse, now standard in 2.7 and beyond. 
it implements a standard command line argument parser with various argument options,
a standard usage and help, and an error termination mechanism do-usage_and_die.

attributes:
all arguments received from the commandline using .add_argument will be
avalable within the .args attribute of object instantiated from CommandLine.
For example, if myCommandLine is an object of the class, and requiredbool was
set as an option using add_argument, then myCommandLine.args.requiredbool will
name that option.

'''

def __init__(self, inOpts=None):
    '''
    CommandLine constructor.
    Implements a parser to interpret the command line argv string using argparse.
    '''

    import argparse
    self.parser = argparse.ArgumentParser(description = 'Program prolog - a brief description of what this thing does', 
                                         epilog = 'Program epilog - some other stuff you feel compelled to say', 
                                         add_help = True, #default is True 
                                         prefix_chars = '-', 
                                         usage = '%(prog)s [options] -option1[default] <input >output'
                                         )
    self.parser.add_argument('inFile', action = 'store', help='input file name')
    self.parser.add_argument('outFile', action = 'store', help='output file name')
    self.parser.add_argument('-lG', '--longestGene', action = 'store', nargs='?', const=True, default=False, help='longest Gene in an ORF')
    self.parser.add_argument('-mG', '--minGene', type=int, choices= (0, 100, 200, 300, 500, 1000), action = 'store', help='minimum Gene length')
    self.parser.add_argument('-s', '--start', action = 'append', nargs='?', help='start Codons') #allows multiple list options
    self.parser.add_argument('-st', '--stop', action = 'append', nargs='?', help='stop Codons') #allows multiple list options
    self.parser.add_argument('-v', '--version', action='version', version='%(prog)s 0.1')  
    if inOpts is None :
        self.args = self.parser.parse_args()
    else :
        self.args = self.parser.parse_args(inOpts)

C:\Users\Zach\Documents\UCSC\BME 160\Lab 5>python findORFsCmdLine.py --    minGene=3
00 --longestGene --start=ATG --stop=TAG --stop=TGA --stop=TAA <tass2.fa     >result.
txt
usage: findORFsCmdLine.py [options] -option1[default] <input >output
findORFsCmdLine.py: error: the following arguments are required: inFile,     outFile

Answer 1

The error tells you that you did not provide inFile and outFile . This seems confusing because you did indeed provide <tass2.fa and >result.txt on the command line.

On the command line < and > have special meaning. <tass2.fa is handled by bash (or whichever shell you use) and it opens the file tass2.fa and sends the contents to your program over stdin . It then removes that from the list of command line arguments because bash has already taken care of it.

A similar thing happens with >result.txt where any output from your file that normally goes to stdout such as print calls will be written to that file. Again bash handles this so your program never gets the argument from the command line.

To make sure the filenames go to your program you need to remove the < and > symbols.

---

In addition to that, the way you are call add_argument for inFile and outFile is not correct. Using action='store' simply stores the value of the argument under the given name. This is the default action so doing that is redundant.

You need to tell add_argument that these are file types. Then you can use these as files and read and write as you desire.

parser.add_argument('inFile', type=argparse.FileType('r'))
parser.add_argument('outFile', type=argparse.FileType('w'))

If you wish to allow these arguments to be optional and use stdin and stdout automatically if they do not supply a filename then you can do this:

parser.add_argument('inFile', type=argparse.FileType('r'),
    nargs='?', default=sys.stdin)
parser.add_argument('outFile', type=argparse.FileType('w'),
    nargs='?', default=sys.stdout)

---

You say you are writing a program that reads from a file and writes to a new file using the command line and go on to say that you are trying to redirect these files to stdin and stdout.

If it is really your intention to redirect the input and output files using the shell with the > and < operators, then you do not need to call add_argument with outFile at all. Just let the shell handle it. Remove that line from your program and use print or similar to send your content to stdout and that file will be created. You will still need the call add_argument('inFile', ... .