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Fixing stop codon 1/3 length issue

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Auden Cote-L'Heureux 2023-11-27 14:09:53 -05:00 committed by GitHub
parent 4e1ceae627
commit 0faa9f0b14
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GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 6 additions and 2 deletions
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8
PTL1/Genomes/Scripts/4_CountOGsDiamond.py
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@ -280,7 +280,7 @@ def update_fasta(args):
og_prefix = rec.split(og_number)[0][-4:] og_prefix = rec.split(og_number)[0][-4:]
og = og_prefix + og_number og = og_prefix + og_number
if len(updated_prot_name[rec]) > 0.33*OGLenDB[og] and len(updated_prot_name[rec]) < 1.5*OGLenDB[og]: if 3*len(updated_prot_name[rec]) > OGLenDB[og] and len(updated_prot_name[rec]) < 1.5*OGLenDB[og]:
w.write('>' + rec + '\n' + updated_prot_name[rec] + '\n\n') w.write('>' + rec + '\n' + updated_prot_name[rec] + '\n\n')
with open(args.ntd_out,'w+') as x: with open(args.ntd_out,'w+') as x:
@ -289,7 +289,11 @@ def update_fasta(args):
og_prefix = rec.split(og_number)[0][-4:] og_prefix = rec.split(og_number)[0][-4:]
og = og_prefix + og_number og = og_prefix + og_number
if len(updated_ntd_name[rec]) > OGLenDB[og] and len(updated_ntd_name[rec]) < 4.5*OGLenDB[og]: ntd_len = len(updated_ntd_name[rec])
if updated_ntd_name[rec].lower().endswith('tag') or updated_ntd_name[rec].lower().endswith('tga') or updated_ntd_name[rec].lower().endswith('taa'):
ntd_len = ntd_len - 3
if ntd_len > OGLenDB[og] and ntd_len < 4.5*OGLenDB[og]:
x.write('>' + rec + '\n' + updated_ntd_name[rec] + '\n\n') x.write('>' + rec + '\n' + updated_ntd_name[rec] + '\n\n')