Python packages

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Running scripts

Running a Python script is very easy, simply call:

python script.py [arguments]

You can try it with one of mine.

Genereal strucuture

This is the script we just ran. In general:

• import things at the top
• define your main function
• define all of your other functions
  • should be as small as possible
  • should take as few inputs as possible

• call the main function using: if __name__ == '__main__':

    import random
    import sys
  
    def main():   
        goal_gcs = calc_goal_gcs(length, gc_content)
        bases = make_rand_oligo(length, goal_gcs)
        gc_count = count_gc(bases)
        new_oligo = check_gc(gc_count, goal_gcs, bases)
  
    def calc_goal_gcs(length, gc_content):
        goal_gcs = int(length*gc_content)
        return goal_gcs
  
    def make_rand_oligo(length, goal_gcs):
        bases = []
        for i in range(length):
            rand_int = random.randint(1, length)
            if rand_int <= goal_gcs:
                if rand_int % 2 == 0:
                    new_base = 'G'
                else:
                    new_base = 'C'
            else:
                if rand_int % 2 == 0:
                    new_base = 'A'
                else:
                    new_base = 'T'
            bases.append(new_base)
        return bases
  
    def count_gc(bases):
        gc_count = 0
        for base in bases:
            if base == 'G':
                gc_count += 1
            elif base == 'C':
                gc_count += 1
            else:
                continue
        return gc_count    
  
    def check_gc(gc_count, goal_gcs, bases):
        if gc_count == goal_gcs:
            new_oligo = ''.join(bases)
            print(new_oligo)
            return new_oligo
        else:
            main()
  
    if __name__ == '__main__':
        length = int(sys.argv[1])
        gc_content = (float(sys.argv[2]))/100
        main()
  

Arguments

There are two main ways to input arguments into your script. Either as positional arguments (as above) or with argparse(preferred way)

1. Positional arguments are simply inputed after the name of the script and then can be called inside the script using sys.argv[1]. The 0 index is the script name itself.
2. Argparse takes a little more time to set up, but allows you to make flags, require arguments and types, and easily collect all of your inputs. There are plenty of examples online of how to use this.

   PEP8

   If you are really concerned about your code being “up to snuff”, you can adhere to the PEP8 guidelines. There are even programs that will check your work to see if you are adhering to them.

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