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Headers in 3_AssignOGs.py

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Auden Cote-L'Heureux 2024-01-20 13:50:41 -05:00 committed by GitHub
parent 559eee63f9
commit 9b02c0074c
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1 changed files with 1 additions and 36 deletions
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PTL1/Transcriptomes/Scripts/3_AssignOGs.py
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@ -265,40 +265,7 @@ def update_fasta(args):
with open(args.input_file.replace('.fasta','.LackOG.fasta'),'w+') as x: with open(args.input_file.replace('.fasta','.LackOG.fasta'),'w+') as x:
for i in seqs_without_OG: for i in seqs_without_OG:
x.write(i) x.write(i)
###########################################################################################
###-------------------- Updates Log With OG Assignment Information ---------------------###
###########################################################################################
def update_log(args):
if os.path.isdir('../PostAssembly_Logs/') != True:
os.system('mkdir ../PostAssembly_Logs/')
else:
pass
home_folder = '/'.join(args.input_file.split('/')[:-1]) + '/'
Renamed_TSV = home_folder+args.input_file.split('/')[-1].replace('.fasta','.Renamed_allOGCleanresults.tsv')
keep = [line for line in open(Renamed_TSV).readlines()]
all_ogs = [line.split('\t')[1].split('_')[-1] for line in keep if len(re.split('_OG.{1}_', line.split('\t')[1])) > 1]
total_with_ogs = str(len(all_ogs))
unique_ogs = str(len(set(all_ogs)))
print (color.BOLD +'There are '+color.BLUE +total_with_ogs+' Contigs'+color.END\
+color.BOLD+' that hit '+color.DARKCYAN+unique_ogs+' Unique OGs\n'+color.END)
for Logname in os.listdir(os.curdir+'./PostAssembly_Logs/'):
if Logname.startswith(args.input_file.split('/')[2].split('_WTA')[0]) and Logname.endswith('Log.txt'):
with open('../PostAssembly_Logs/'+Logname,'a') as LogFile:
LogFile.write('Contigs With OG\t'+total_with_ogs+'\tn/a\tn/a\n')
LogFile.write('Unique OGs\t'+unique_ogs+'\tn/a\tn/a\n')
########################################################################################## ##########################################################################################
###--------------------- Cleans up the Folder and Moves Final Files -------------------### ###--------------------- Cleans up the Folder and Moves Final Files -------------------###
@ -348,8 +315,6 @@ def main():
update_fasta(args) update_fasta(args)
#update_log(args)
clean_up(args) clean_up(args)
next_script(args) next_script(args)