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Updating arg parsing in tip counting script

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Auden Cote-L'Heureux 2023-10-24 11:15:37 -04:00 committed by GitHub
parent 2280edaf5a
commit 9d07bca28c
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1 changed files with 14 additions and 23 deletions
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37
Utilities/for_trees/count_tips.py
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@ -1,6 +1,6 @@
''' '''
Author: Auden Cote-L'Heureux Author: Auden Cote-L'Heureux
Last updated: 06/14/23 by Elinor Last updated: 10/24/23
Motivation: Count the number of occurences of each taxa in each OG in a post guidance file Motivation: Count the number of occurences of each taxa in each OG in a post guidance file
Dependencies: Bio python, os, sys Dependencies: Bio python, os, sys
Inputs: Directory of postguidance files Inputs: Directory of postguidance files
@ -15,31 +15,22 @@ from Bio import SeqIO
def get_args(): def get_args():
in_dir = '' parser = argparse.ArgumentParser(
prog = 'Tip counting script',
if('--input' in sys.argv or '-i' in sys.argv): description = "Updated Oct 24th, 2023 by Auden Cote-L'Heureux."
try: )
if('--input' in sys.argv):
in_dir = sys.argv[sys.argv.index('--input') + 1] parser.add_argument('-i', '--input', type = str, required = True, help = 'Path to the folder containing the input trees')
else: args = parser.parse_args()
in_dir = sys.argv[sys.argv.index('-i') + 1]
except IndexError:
print('\nError: Something went wrong went parsing the arguments... maybe you forgot to input an input directory of trees?\n')
print('\nPlease input a folder of .tre files:\n\n\tpython count_tips.py --input <path/to/folder>\n')
exit()
else:
print('\nPlease input a folder of .tre files:\n\n\tpython count_tips.py --input <path/to/folder>\n')
exit()
if(args.input.endswith('/')):
args.input = args.input[:-1]
if(in_dir.endswith('/')): if(not os.path.isdir(args.input)):
in_dir = in_dir[:-1] print('\nThe input folder (--input) could not be found. Make sure you have given the correct path.\n')
if(not os.path.isdir(in_dir)):
print('\nPlease input a folder of .tre files:\n\n\tpython count_tips.py --input <path/to/folder>\n')
exit() exit()
return in_dir return args.input
def count_tips(in_dir): def count_tips(in_dir):
@ -79,4 +70,4 @@ def main():
count_tips(in_dir) count_tips(in_dir)
main() main()