1

The command line to run my Python script is:

./parse_ms.py inputfile 3 2 2 2

the arguments are an input, number 3 is the number of samples of my study each with 2 individuals.

In the script, I indicate the arguments as follows:

inputfile = open(sys.argv[1], "r")
nsam = int(sys.argv[2])
nind1 = int(sys.argv[3])
nind2 = int(sys.argv[4])
nind3 = int(sys.argv[5])

However, the number of samples may vary. I can have:

./parse_ms.py input 4 6 8 2 20

in this case, I have 4 samples with 6, 8, 2 and 20 individuals in each.

It seems inefficient to add another sys.argv everything a sample is added. Is there a way to make this more general? That is, if I write nsam to be equal to 5, automatically, Python excepts five numbers to follow for the individuals in each sample.

Homap
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  • `samples = sys.argv[3:]`? or use `argparse` to parse a flag instead. Or use `shlex.split` on a group or numbers enclosed in `"` – Torxed Sep 28 '17 at 12:40
  • `len(sys.arvg)` gives you the length of the input list (+1 for the executable name), so you can skip the first argument and can use a for loop with a list for arbitrary amount of arguments. There are libraries which can help you with argument parsing. – syntonym Sep 28 '17 at 12:41
  • @Torxed how can we use argparse for this scenario please ? – dada May 29 '20 at 14:58

2 Answers2

8

You can simply slice off the rest of sys.argv into a list. e.g.

inputfile = open(sys.argv[1], "r")
num_samples = int(sys.argv[2])
samples = sys.argv[3:3+num_samples]

Although if that is all your arguments, you can simply not pass a number of samples and just grab everything.

inputfile = open(sys.argv[1], "r")
samples = sys.argv[2:]

Samples can be converted to the proper datatype afterward.

Also, look at argparse for a nicer way of handling command line arguments in general.

0

You can have a list of ninds and even catch expections doing the following

try:
    ninds = [int(argv[i+3]) for i in range(int(argv[2]))]
except IndexError:
    print("Error. Expected %s samples and got %d" %(argv[2], len(argv[3:])))
Arthur Gouveia
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