YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2026-02-10 20:40:25 +08:00
Code Issues Packages Projects Releases Wiki Activity

Updating arg parsing in tip counting script

Browse Source
This commit is contained in:
Auden Cote-L'Heureux 2023-10-24 11:15:37 -04:00 committed by GitHub
parent 2280edaf5a
commit 9d07bca28c
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 14 additions and 23 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

37
Utilities/for_trees/count_tips.py
View File

@ -1,6 +1,6 @@
'''
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
Dependencies: Bio python, os, sys
Inputs: Directory of postguidance files
@ -15,31 +15,22 @@ from Bio import SeqIO
def get_args():
in_dir = ''
if('--input' in sys.argv or '-i' in sys.argv):
try:
if('--input' in sys.argv):
in_dir = sys.argv[sys.argv.index('--input') + 1]
else:
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()
parser = argparse.ArgumentParser(
prog = 'Tip counting script',
description = "Updated Oct 24th, 2023 by Auden Cote-L'Heureux."
)
parser.add_argument('-i', '--input', type = str, required = True, help = 'Path to the folder containing the input trees')
args = parser.parse_args()
if(args.input.endswith('/')):
args.input = args.input[:-1]
if(in_dir.endswith('/')):
in_dir = in_dir[:-1]
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')
if(not os.path.isdir(args.input)):
print('\nThe input folder (--input) could not be found. Make sure you have given the correct path.\n')
exit()
return in_dir
return args.input
def count_tips(in_dir):
@ -79,4 +70,4 @@ def main():
count_tips(in_dir)
main()
main()