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82 lines
2.1 KiB
Python
82 lines
2.1 KiB
Python
'''
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Author: Auden Cote-L'Heureux
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Last updated: 06/14/23 by Elinor
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Motivation: Count the number of occurences of each taxa in each OG in a post guidance file
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Dependencies: Bio python, os, sys
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Inputs: Directory of postguidance files
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Outputs: CSV file tallying all the counts of taxa in each OG file
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Command line: python count_tips.py --input <dir of postguidance files>
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'''
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import os
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import sys
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from Bio import SeqIO
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def get_args():
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in_dir = ''
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if('--input' in sys.argv or '-i' in sys.argv):
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try:
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if('--input' in sys.argv):
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in_dir = sys.argv[sys.argv.index('--input') + 1]
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else:
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in_dir = sys.argv[sys.argv.index('-i') + 1]
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except IndexError:
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print('\nError: Something went wrong went parsing the arguments... maybe you forgot to input an input directory of trees?\n')
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print('\nPlease input a folder of .tre files:\n\n\tpython count_tips.py --input <path/to/folder>\n')
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exit()
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else:
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print('\nPlease input a folder of .tre files:\n\n\tpython count_tips.py --input <path/to/folder>\n')
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exit()
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if(in_dir.endswith('/')):
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in_dir = in_dir[:-1]
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if(not os.path.isdir(in_dir)):
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print('\nPlease input a folder of .tre files:\n\n\tpython count_tips.py --input <path/to/folder>\n')
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exit()
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return in_dir
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def count_tips(in_dir):
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count_data = { }
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for file in os.listdir(in_dir):
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if(file.endswith('.fas')):
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fname = in_dir + '/' + file
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count_data.update({ file : { } })
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tips = [record.id[:10] for record in SeqIO.parse(in_dir+'/'+file, 'fasta')]
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for tip in tips:
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tip = tip.strip()
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if(tip[:10] not in count_data[file]):
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count_data[file].update({ tip[:10] : 0 })
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count_data[file][tip[:10]] += 1
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taxa = sorted(list(dict.fromkeys([tax for file in count_data for tax in count_data[file]])))
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with open('tip_count_data.csv', 'w') as o:
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o.write(',' + ','.join(taxa) + '\n')
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for file in count_data:
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o.write(file)
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for tax in taxa:
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if(tax in count_data[file]):
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o.write(',' + str(count_data[file][tax]))
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else:
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o.write(',0')
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o.write('\n')
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def main():
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in_dir = get_args()
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count_tips(in_dir)
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main() |