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Updating annotations 2b_Identify_Proks.py

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Auden Cote-L'Heureux 2024-01-16 14:32:50 -05:00 committed by GitHub
parent c77e63eb74
commit ff9a419c4e
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1 changed files with 1 additions and 28 deletions
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PTL1/Transcriptomes/Scripts/2b_Identify_Proks.py
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@ -328,31 +328,6 @@ def compare_hits(args):
return str(len(Euk_Fasta)), str(len(Prok_Fasta)), str(len(Und_Fasta)) return str(len(Euk_Fasta)), str(len(Prok_Fasta)), str(len(Und_Fasta))
###########################################################################################
###----------------------- Updates Log of Prok vs Euk Comparisons ----------------------###
###########################################################################################
def update_log(args, Euk_Contigs, Prok_Contigs, Und_Contigs):
if os.path.isdir('../PostAssembly_Logs/') != True:
os.system('mkdir ../PostAssembly_Logs/')
else:
pass
print (color.BOLD +'\n\nThere are '+color.RED+Prok_Contigs+' Strongly Prokaryotic contigs'+color.END\
+color.BOLD+',\n'+color.ORANGE+Euk_Contigs+' Strongly Eukaryotic contigs'+color.END\
+color.BOLD+',\nand '+color.PURPLE+Und_Contigs+' Undetermined Contigs\n'+color.END\
+color.BOLD+'in '+args.input_file.split('/')[-1]+color.END)
for Logname in os.listdir(os.curdir+'./PostAssembly_Logs/'):
if Logname.startswith(args.input_file.split('/')[-1].split('_No')[0]) and Logname.endswith('Log.txt'): # ACL - ???
with open('../PostAssembly_Logs/'+Logname,'a') as Logfilename:
Logfilename.write('Prokaryotic Contigs\t'+Prok_Contigs+'\tn/a\tn/a\n')
Logfilename.write('Eukaryotic Contigs\t'+Euk_Contigs+'\tn/a\tn/a\n')
Logfilename.write('Undetermined Contigs\t'+Und_Contigs+'\tn/a\tn/a\n')
########################################################################################### ###########################################################################################
###-------------------------------- Next Script Message --------------------------------### ###-------------------------------- Next Script Message --------------------------------###
########################################################################################### ###########################################################################################
@ -393,8 +368,6 @@ def main():
Euk_Contigs, Prok_Contigs, Und_Contigs = compare_hits(args) Euk_Contigs, Prok_Contigs, Und_Contigs = compare_hits(args)
#update_log(args, Euk_Contigs, Prok_Contigs, Und_Contigs)
clean_up(args) clean_up(args)
next_script(args) next_script(args)