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57 lines
1.8 KiB
Python
57 lines
1.8 KiB
Python
#Author, date: ACL June 8 2023
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#Motivation: Get record of OG presence across taxa from ReadyToGo files
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#Intent: Create a spreadsheet summarizing OG presence
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#Inputs: A folder of ReadyToGo files
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#Outputs: Spreadsheet.
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#Example: Python SharedOGs.py ReadyToGo_AA
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import os, sys
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from Bio import SeqIO
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from tqdm import tqdm
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input_dir = sys.argv[1]
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print('\nCreating a record of taxa per OG...')
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taxa_by_og = { }
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for file in tqdm(os.listdir(input_dir)):
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if file.split('.')[-1] in ('fasta', 'faa', 'fna', 'fa'):
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tax = file[:10]
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for rec in SeqIO.parse(input_dir + '/' + file, 'fasta'):
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if rec.id[-10:] not in taxa_by_og:
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taxa_by_og.update({ rec.id[-10:] : [] })
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taxa_by_og[rec.id[-10:]].append(tax)
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print('\nWriting output file...')
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all_taxa = sorted(list(dict.fromkeys([tax for og in taxa_by_og for tax in taxa_by_og[og]])))
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all_maj = sorted(list(dict.fromkeys([tax[:2] for og in taxa_by_og for tax in taxa_by_og[og]])))
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with open('OGSharedness.csv', 'w') as o:
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o.write('OG,Sequences,Species,Paralogness,MinorClades,MajorClades,' + ','.join(all_maj) + ',' + ','.join(all_taxa) + '\n')
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for og in tqdm(taxa_by_og):
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og_majs = list(dict.fromkeys([tax[:2] for tax in taxa_by_og[og]]))
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og_taxa = list(dict.fromkeys(taxa_by_og[og]))
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o.write(og + ',' + str(len(taxa_by_og[og])) + ',' + str(len(list(dict.fromkeys(taxa_by_og[og])))) + ',' + str(len(taxa_by_og[og])/len(list(dict.fromkeys(taxa_by_og[og])))) + ',' + str(len(list(dict.fromkeys([tax[:5] for tax in taxa_by_og[og]])))) + ',' + str(len(list(dict.fromkeys([tax[:2] for tax in taxa_by_og[og]])))))
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for maj in all_maj:
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if maj in og_majs:
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o.write(',' + str(len([tax for tax in og_taxa if tax[:2] == maj])))
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else:
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o.write(',0')
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for tax in all_taxa:
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if tax in taxa_by_og[og]:
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o.write(',' + str(taxa_by_og[og].count(tax)))
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else:
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o.write(',0')
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o.write('\n')
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