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Update CountTaxonOccurence.py
updated to include summary of major and minor clades, and to allow target minor clade list
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@ -1,13 +1,15 @@
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'''
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Author: Auden Cote-L'Heureux
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Last updated: 10/24/23
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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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Author: Auden Cote-L'Heureux, Laura Katz and ChatGPT
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Last updated: June 9th, 2024
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Motivation: Count the number of occurrences 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 CountTaxonOccurence.py --input <dir of postguidance files>
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Inputs: Directory of postguidance files
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Optional: use the --minor flag and include a file named focal_minors.txt in same folder (do not put file name in command line). This file should be csv of targets (Am_tu, Sr_rh, Sr_ci)
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Outputs: CSV file tallying all the counts of taxa in each OG file plus minor and major clade tallies
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Command line: python3 CountTaxonOccurence_faster_minor.py --input <dir of postguidance files> --minor
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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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@ -15,60 +17,108 @@ import argparse
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def get_args():
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parser = argparse.ArgumentParser(
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prog = 'Taxon occurence counting script',
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description = "Updated Oct 24th, 2023 by Auden Cote-L'Heureux."
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)
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parser.add_argument('-i', '--input', type = str, required = True, help = 'Path to the folder containing the aligned/unaligned fasta files')
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args = parser.parse_args()
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if(args.input.endswith('/')):
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args.input = args.input[:-1]
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if(not os.path.isdir(args.input)):
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print('\nThe input folder (--input) could not be found. Make sure you have given the correct path.\n')
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exit()
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return args.input
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parser = argparse.ArgumentParser(
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prog = 'Taxon occurrence counting script',
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description = "Updated June 9, 2024"
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)
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parser.add_argument('-i', '--input', type = str, required = True, help = 'Path to the folder containing the aligned/unaligned fasta files')
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parser.add_argument('--minor', action='store_true', help = 'Flag to use focal minor clades from focal_minors.txt')
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args = parser.parse_args()
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if(args.input.endswith('/')):
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args.input = args.input[:-1]
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if(not os.path.isdir(args.input)):
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print('\nThe input folder (--input) could not be found. Make sure you have given the correct path.\n')
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exit()
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return args.input, args.minor
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def count_tips(in_dir):
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def count_tips(in_dir, use_focal_minors):
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focal_minors = []
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if use_focal_minors:
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try:
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with open('focal_minors.txt', 'r') as f:
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focal_minors = f.read().strip().split(',')
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focal_minors = [minor.strip() for minor in focal_minors]
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except FileNotFoundError:
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print('A file called focal_minors.txt must be included in the folder with your script. This file should have a csv of target minor clades such as "Am_tu, Sr_ci, Sr_rh"')
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exit()
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count_data = {}
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major_clades = set()
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minor_clades = set()
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for file in os.listdir(in_dir):
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if file.split('.')[-1] in ('fasta', 'fas', 'faa', 'fna'):
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fname = os.path.join(in_dir, file)
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count_data[file] = {}
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# Use SeqIO.index for faster access
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seq_index = SeqIO.index(fname, "fasta")
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tips = [seq_index[record_id].id[:10] for record_id in seq_index]
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for tip in tips:
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major_clade = tip[:2]
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minor_clade = tip[:5]
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if use_focal_minors:
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if minor_clade not in focal_minors:
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continue
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major_clades.add(major_clade)
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minor_clades.add(minor_clade)
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if tip not in count_data[file]:
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count_data[file][tip] = 0
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count_data[file][tip] += 1
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if use_focal_minors:
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# Filter major and minor clades based on focal minors
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major_clades = sorted({minor[:2] for minor in focal_minors})
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minor_clades = sorted(focal_minors)
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else:
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major_clades = sorted(major_clades)
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minor_clades = sorted(minor_clades)
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taxa = sorted({tax for file_data in count_data.values() for tax in file_data})
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# Generate output file name based on input folder name
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folder_name = os.path.basename(in_dir)
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output_file_name = folder_name + "_TaxonOccurrence.csv"
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with open(output_file_name, 'w') as o:
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o.write(',' + ','.join(major_clades + minor_clades + taxa) + '\n')
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for file in count_data:
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o.write(file)
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major_clade_counts = {clade: 0 for clade in major_clades}
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minor_clade_counts = {clade: 0 for clade in minor_clades}
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for tax, count in count_data[file].items():
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major_clade_counts[tax[:2]] += count
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minor_clade_counts[tax[:5]] += count
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for clade in major_clades:
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o.write(',' + str(major_clade_counts[clade]))
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for clade in minor_clades:
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o.write(',' + str(minor_clade_counts[clade]))
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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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count_data = { }
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for file in os.listdir(in_dir):
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if file.split('.')[-1] in ('fasta', 'fas', 'faa', 'fna'):
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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('TaxonOccurrence.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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in_dir, use_focal_minors = get_args()
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count_tips(in_dir, use_focal_minors)
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main()
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