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Added annotation to 4_CountOGsDiamond.py

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Auden Cote-L'Heureux 2023-09-18 10:04:25 -04:00 committed by GitHub
parent 8e561dc735
commit 106b2e2d89
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1 changed files with 4 additions and 2 deletions
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PTL1/Genomes/Scripts/4_CountOGsDiamond.py
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@ -1,6 +1,6 @@
#!/usr/bin/env python3.5 #!/usr/bin/env python3.5
##__Updated__: 19_09_2017 ##__Updated__: 18_09_2023 (by ACL)
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com ##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
##__Usage__: python 3g_GCodeTranslate.py --help ##__Usage__: python 3g_GCodeTranslate.py --help
@ -246,6 +246,7 @@ def update_fasta(args):
hook_fasta = [file for file in os.listdir(args.databases + '/db_OG') if file.endswith('.fasta')][0] hook_fasta = [file for file in os.listdir(args.databases + '/db_OG') if file.endswith('.fasta')][0]
#Getting average length in Hook: addition per 9/2023 update
OGLenDB = {} OGLenDB = {}
for rec in SeqIO.parse(args.databases + '/db_OG/' + hook_fasta, 'fasta'): for rec in SeqIO.parse(args.databases + '/db_OG/' + hook_fasta, 'fasta'):
if rec.id[-10:] not in OGLenDB: if rec.id[-10:] not in OGLenDB:
@ -272,6 +273,7 @@ def update_fasta(args):
updated_prot_name = { keep_dict[i.description] : str(i.seq).rstrip('*') for i in protFasta if i.description in keep_dict.keys() } updated_prot_name = { keep_dict[i.description] : str(i.seq).rstrip('*') for i in protFasta if i.description in keep_dict.keys() }
updated_ntd_name = { keep_dict[i.description] : str(i.seq).rstrip('*') for i in ntdFasta if i.description in keep_dict.keys() } updated_ntd_name = { keep_dict[i.description] : str(i.seq).rstrip('*') for i in ntdFasta if i.description in keep_dict.keys() }
#Additional length filter here per 9/2023 update
with open(args.aa_out,'w+') as w: with open(args.aa_out,'w+') as w:
for rec in updated_prot_name: for rec in updated_prot_name:
og_number = re.split('OG.{1}_', rec)[1][:6] og_number = re.split('OG.{1}_', rec)[1][:6]