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Auden Cote-L'Heureux 2023-06-12 13:37:47 -04:00 committed by GitHub
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Utilities/for_fastas/sharedOGs.py Normal file
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#Author, date: ACL June 8 2023
#Motivation: Get record of OG presence across taxa from ReadyToGo files
#Intent: Create a spreadsheet summarizing OG presence
#Inputs: A folder of ReadyToGo files
#Outputs: Spreadsheet
#Example: Python sharedOGs.py ReadyToGo_AA
import os, sys
from Bio import SeqIO
from tqdm import tqdm
input_dir = sys.argv[1]
print('\nCreating a record of taxa per OG...')
taxa_by_og = { }
for file in tqdm(os.listdir(input_dir)):
if file.split('.')[-1] in ('fasta', 'faa', 'fna', 'fa'):
tax = file[:10]
for rec in SeqIO.parse(input_dir + '/' + file, 'fasta'):
if rec.id[-10:] not in taxa_by_og:
taxa_by_og.update({ rec.id[-10:] : [] })
taxa_by_og[rec.id[-10:]].append(tax)
print('\nWriting output file...')
all_taxa = sorted(list(dict.fromkeys([tax for og in taxa_by_og for tax in taxa_by_og[og]])))
all_maj = sorted(list(dict.fromkeys([tax[:2] for og in taxa_by_og for tax in taxa_by_og[og]])))
with open('OGSharedness.csv', 'w') as o:
o.write('OG,Sequences,Species,Paralogness,MinorClades,MajorClades,' + ','.join(all_maj) + ',' + ','.join(all_taxa) + '\n')
for og in tqdm(taxa_by_og):
og_majs = list(dict.fromkeys([tax[:2] for tax in taxa_by_og[og]]))
og_taxa = list(dict.fromkeys(taxa_by_og[og]))
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]])))))
for maj in all_maj:
if maj in og_majs:
o.write(',' + str(len([tax for tax in og_taxa if tax[:2] == maj])))
else:
o.write(',0')
for tax in all_taxa:
if tax in taxa_by_og[og]:
o.write(',' + str(taxa_by_og[og].count(tax)))
else:
o.write(',0')
o.write('\n')