reorganize sim output

[wuben2602]

reorganizes text output of outbreak sim to csv file

[BoPeng]

Please first convert the script to a proper python program with command line options in the style of

def function_to_do_something(parameter):
    ...

if __name__ == '__main__':
    parser = argparse.ArgumentParser....
    args = ...
    function_to_do_something(args.whatever)

[BoPeng]

Seems not completed yet. Let me know when it is ready for review.

[wuben2602]

I just rewrote the script to add the command line options

[BoPeng]

I wrote a few comments. I would suggest that you write a few functions to

1. Identify time points (rows of the table)
2. identify names with these time points (rows that can be converted)
3. expand these rows to columns of the csv file depending on the values of these rows. proper column names need to be derived.

This will make your script easier to follow.

[wuben2602]

This is my completed code as of 7/1. I adjusted the code quite a bit. The order of the columns are not the same as in the text file.

[wuben2602]

These are my most recent changes as of 7/6. I didn't really understand how to get an argument to be '-' and I just tried to the best of my ability to allow an option to be the standard input. If you could clarify, that would be greatly appreciated.

[wuben2602]

argparse doesn't accept the use of '-' as a parameter, so I had to use '-s'. If reorganize.py -s is called, then it'll read from standard input. With both input and standard input, standard output or file output can be chosen

[BoPeng]

I meant, either

script -i -

or

script --input -

or

script -

In the first two cases, the parameters should be

add_argument('-i', '--input')

as named parameter. In the last case, the parameter should be

add_argument('input')

as positional argument.

[wuben2602]

changes as of 7/6