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EukPhylo/PTL1/Transcriptomes/Scripts/2b_Identify_Proks.py
Auden Cote-L'Heureux c77e63eb74
Updating header in 2b_Identify_Proks.py
2024-01-16 14:32:26 -05:00

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Python
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# Last updated Sept. 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux
# This script is intended to identify likely prokarotic (contaminant) sequences. It does
# this by similarity-searching against a reference database of eukaryote and prokaryote
# sequences, and it labels the output sequences with an "E" (likely eukaryotic), "P" (likely
# prokaryotic) or "U" (Unknown) in the sequence ID. This is done by comparing e-values: if
# a sequence hits a eukaryotic sequence with an e-value >100 times that of its best hit
# to a prokaryotic sequence, it is labeled with an "E"; if it's best hit to a prokaryotic
# sequence has an e-value >1000 times that of its best hit to a eukaryotic sequence, it is
# labeled with a "P". Anything else gets a "U". This script should be run as part of the
# PhyloToL version 6 Part 1 pipeline using the script wrapper.py.
# Prior to running this script, ensure that you have run scripts 1a (and optionally
# script 1b) and 2a, and that your prokaryote and reference databases (or the default
# ones provided on the GitHub) is in the proper database folder
# (Databases/BvsE/eukout.dmnd and micout.dmnd).
import argparse, os, sys
from argparse import RawTextHelpFormatter,SUPPRESS
from distutils import spawn
from Bio import SeqIO
#------------------------------ Colors For Print Statements ------------------------------#
class color:
PURPLE = '\033[95m'
CYAN = '\033[96m'
DARKCYAN = '\033[36m'
ORANGE = '\033[38;5;214m'
BLUE = '\033[94m'
GREEN = '\033[92m'
YELLOW = '\033[93m'
RED = '\033[91m'
BOLD = '\033[1m'
UNDERLINE = '\033[4m'
END = '\033[0m'
#------------------------------- Main Functions of Script --------------------------------#
###########################################################################################
###---------------------------- UPDATE DIAMOND PATH BELOW! -----------------------------###
###########################################################################################
## IF Diamond is IN YOUR PATH then no updating is needed...
def check_diamond_path():
diamond_path = ''
if diamond_path == '':
diamond_path = spawn.find_executable("diamond")
#diamond_path = '/path/to/diamond'
else:
pass
if diamond_path == None:
print (color.BOLD + '\n\nPlease open this script and check that you have included'\
+' the PATH to the'+color.BLUE+' "Diamond" '+color.END+color.BOLD+'executable.\n\n'+color.END)
print (color.BOLD+color.BLUE+'LOOK FOR:\n\n'+color.RED\
+'#------------------------------ UPDATE DIAMOND PATH BELOW! -------------------------------#'\
+color.BLUE+'\n\nThis is somewhere around lines 50 - 80...\n\n'+color.END)
sys.exit()
else:
pass
return diamond_path
###########################################################################################
###--------------------- Parses and Checks Command-Line Arguments ----------------------###
###########################################################################################
def check_args():
parser = argparse.ArgumentParser(description=
color.BOLD + '\nThis script will categorize Contigs as'+color.ORANGE+' STRONGLY '+color.END\
+color.BOLD+color.RED+'Eukaryotic \nOR Prokaryotic'+color.END+color.BOLD+' using a set of Proteins'\
' from diverse\n'+color.ORANGE+'Eukaryotes, Bacteria and Archaea'+color.END\
+color.BOLD+'.'+color.END+usage_msg(), usage=SUPPRESS,formatter_class=RawTextHelpFormatter)
required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END)
required_arg_group.add_argument('--input_file','-in', action='store',
help=color.BOLD+color.GREEN+'Fasta file of Nucleotide sequences (with rRNAs removed)'+color.END)
required_arg_group.add_argument('--databases','-d', action='store',
help=color.BOLD+color.GREEN+"Path to databases"+color.END)
optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
optional_arg_group.add_argument('-author', action='store_true',
help=color.BOLD+color.GREEN+' Print author contact information\n'+color.END)
if len(sys.argv[1:]) == 0:
print (parser.description)
print ('\n')
sys.exit()
args = parser.parse_args()
quit_eval = return_more_info(args)
if quit_eval > 0:
sys.exit()
return args
###########################################################################################
###------------------------------- Script Usage Message --------------------------------###
###########################################################################################
def usage_msg():
return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 2b_remove_Bact.py --input_file'\
' ../Op_me_Xxma/Op_me_Xxma_NorRNAseqs.fasta'+color.END)
##########################################################################################
###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------###
##########################################################################################
def return_more_info(args):
valid_arg = 0
author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\
' maurerax@gmail.com\n\n'+color.END)
if args.author == True:
print (author)
valid_arg += 1
print(args.input_file)
if args.input_file != None:
if os.path.isfile(args.input_file) != False:
if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])):
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
valid_arg += 1
elif args.input_file.endswith('NorRNAseqs.fasta') != True:
print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\
' with '+color.GREEN+'2a_remove_rRNA.py '+color.END+color.BOLD+'are valid\n\n'\
'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\
'"NorRNAseqs.fas"\n\n'+color.END)
valid_arg += 1
else:
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
valid_arg += 1
if os.path.isdir(args.databases + '/db_BvsE') != True:
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
+color.ORANGE+'db_BvsE Folder!\n\n'+color.END+color.BOLD+'Ensure that this folder '\
'can be found in the main '+color.ORANGE+'Databases Folder'+color.END+color.BOLD\
+'\n\nThen try once again.')
valid_arg += 1
elif os.path.isfile(args.databases + '/db_BvsE/eukout.dmnd') != True:
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
'Diamond formatted '+color.ORANGE+'Eukaryotic Protein database!\n\n'+color.END+color.BOLD+\
'Ensure that it can be found in the '+color.ORANGE+'db_BvsE folder'+color.END+\
color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\
color.END+color.BOLD+'\n\nThen try once again.'+color.END)
elif os.path.isfile(args.databases + '/db_BvsE/micout.dmnd') != True:
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
'Diamond formatted '+color.ORANGE+'Bacterial/Archaeal Protein database!\n\n'+color.END+color.BOLD+\
'Ensure that it can be found in the '+color.ORANGE+'db_BvsE folder'+color.END+\
color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\
color.END+color.BOLD+'\n\nThen try once again.'+color.END)
valid_arg += 1
return valid_arg
###########################################################################################
###--------------------------- Does the Inital Folder Prep -----------------------------###
###########################################################################################
def prep_folders(args):
BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
if os.path.isdir(BvE_folder) != True:
os.system('mkdir '+BvE_folder)
###########################################################################################
###---------------- Runs Diamond on Bact and Euk small RefSeq Databases ----------------###
###########################################################################################
def ublast_BvE(args, diamond_path):
BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
mic_output = args.input_file.split('/')[-1]+'micresults.'
euk_output = args.input_file.split('/')[-1]+'eukresults.'
print(color.BOLD+'\n\n"BLAST"-ing against PROK database using DIAMOND: ' + color.DARKCYAN + 'micout.dmnd' + color.END + '\n\n')
Prok_diamond_cmd = diamond_path + ' blastx -q ' + args.input_file + ' --max-target-seqs 1 -d ' + args.databases + '/db_BvsE/micout.dmnd --evalue 1e-5 --threads 60 --outfmt 6 -o ' + BvE_folder + 'allmicresults.tsv'
os.system(Prok_diamond_cmd)
print(color.BOLD+'\n\n"BLAST"-ing against EUK database using DIAMOND: ' + color.DARKCYAN + 'eukout.dmnd' + color.END + '\n\n')
Euk_diamond_cmd = diamond_path + ' blastx -q ' + args.input_file + ' --max-target-seqs 1 -d ' + args.databases + '/db_BvsE/eukout.dmnd --evalue 1e-5 --threads 60 --outfmt 6 -o ' + BvE_folder + 'alleukresults.tsv'
os.system(Euk_diamond_cmd)
###########################################################################################
###---------------- Compares Bacterial and Euk Hits for Classification -----------------###
###########################################################################################
def compare_hits(args):
BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
EukDict = {}
ProkDict = {}
CompDict = {}
inFasta = [seq_rec for seq_rec in SeqIO.parse(args.input_file,'fasta')]
for seq_rec in inFasta:
EukDict[seq_rec.description] = ''
ProkDict[seq_rec.description] = ''
CompDict[seq_rec.description] = []
inEukHits = [i for i in open(BvE_folder + 'alleukresults.tsv').readlines()]
inEukHits.sort(key=lambda x: (float(x.split('\t')[-2]), -int(x.split('\t')[3])))
inProkHits = [i for i in open(BvE_folder + 'allmicresults.tsv').readlines()]
inProkHits.sort(key=lambda x: (float(x.split('\t')[-2]), -int(x.split('\t')[3])))
for i in inEukHits:
if EukDict[i.split('\t')[0]] == '':
EukDict[i.split('\t')[0]] = float(i.split('\t')[-2])
for i in inProkHits:
if ProkDict[i.split('\t')[0]] == '':
ProkDict[i.split('\t')[0]] = float(i.split('\t')[-2])
for k in CompDict.keys():
if EukDict[k] != '':
CompDict[k].append(EukDict[k])
else:
CompDict[k].append('no hit')
if ProkDict[k] != '':
CompDict[k].append(ProkDict[k])
else:
CompDict[k].append('no hit')
for k, v in CompDict.items():
### Contigs lacking STRONG Eukaryotic OR Prokaryotic Hits
if v[0] == 'no hit' and v[1] == 'no hit':
CompDict[k].append('UNDETERMINED')
### Contigs lacking STRONG Eukaryotic with a Prokaryotic Hit
elif v[0] != 'no hit' and v[1] == 'no hit':
CompDict[k].append('EUKARYOTIC')
### Contigs with a Eukaryotic but without a Prokaryotic Hit
elif v[0] == 'no hit' and v[1] != 'no hit':
CompDict[k].append('PROKARYOTIC')
### Uses Basic math to determine if contigs with are MORE Eukaryotic than Prokaryotic
else:
try:
prok_euk_ratio = float(v[1])/float(v[0])
euk_prok_ratio = float(v[0])/float(v[1])
if prok_euk_ratio >= 100:
CompDict[k].append('EUKARYOTIC')
elif euk_prok_ratio >= 1000:
CompDict[k].append('PROKARYOTIC')
else:
CompDict[k].append('UNDETERMINED')
except:
CompDict[k].append('divide by zero')
with open(BvE_folder + 'comparisons.txt','w+') as w:
for k, v in CompDict.items():
w.write(k+':'+':'.join([str(i) for i in v])+'\n')
BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
BvE_output_base = BvE_folder+args.input_file.split('/')[-1].split('.fas')[0]
### Gathers the sequences and categorizes them
Euk_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'EUKARYOTIC'), key=lambda x: -int(len(x.seq)))
Prok_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'PROKARYOTIC'), key=lambda x: -int(len(x.seq)))
Und_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'UNDETERMINED'), key=lambda x: -int(len(x.seq)))
Zero_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'divide by zero'), key=lambda x: -int(len(x.seq)))
### Writes out all of the categorized sequences
with open(args.input_file.split('NorRNA')[0] + 'WTA_EPU.fasta', 'w') as epu:
with open(BvE_output_base+'.Not_Bact.fasta','w+') as nb:
for euk_seq in Euk_Fasta:
nb.write('>' + euk_seq.description + '\n' + str(euk_seq.seq) + '\n')
epu.write('>' + euk_seq.description + '_E' + '\n' + str(euk_seq.seq) + '\n')
with open(BvE_output_base+'.Bact_Hit.fasta','w+') as pr:
for prok_seq in Prok_Fasta:
pr.write('>' + prok_seq.description + '\n' + str(prok_seq.seq) + '\n')
epu.write('>' + prok_seq.description + '_P' + '\n' + str(prok_seq.seq) + '\n')
with open(BvE_output_base+'.Undetermined.fasta','w+') as und:
for und_seq in Und_Fasta:
und.write('>' + und_seq.description + '\n' + str(und_seq.seq) + '\n')
epu.write('>' + und_seq.description + '_U' + '\n' + str(und_seq.seq) + '\n')
if len(Zero_Fasta) != 0:
with open(BvE_output_base+'.DivideByZero.fasta','w+') as w:
for zero_seq in Zero_Fasta:
w.write('>' + zero_seq.description + '\n' + str(zero_seq.seq) + '\n')
epu.write('>' + zero_seq.description + '_U' + '\n' + str(zero_seq.seq) + '\n')
else:
pass
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 --------------------------------###
###########################################################################################
def next_script(args):
print (color.BOLD+'\nLook for '+color.DARKCYAN+args.input_file.split('/')[-1]\
.split('NorRNA')[0]+'WTA_EPU.fasta'+color.END+color.BOLD+' in the '\
+args.input_file.split('/')[1]+' Folder\n\n' + color.END)
print (color.BOLD + 'Next Script is: ' + color.GREEN + '3_CountOGsDiamond.py\n\n'+ color.END)
##########################################################################################
###--------------------- Cleans up the Folder and Moves Final Files -------------------###
##########################################################################################
def clean_up(args):
home_folder = '/'.join(args.input_file.split('/')[:-1])
os.system('cp '+home_folder+'/*WTA_EPU.fasta '+home_folder+'/BvE/')
os.system('mv '+home_folder+'/*NorRNA*fasta '+home_folder+'/rRNA_Removal/')
##########################################################################################
###--------------- Checks Command Line Arguments and Calls on Functions ---------------###
##########################################################################################
def main():
usearch_path = check_diamond_path()
args = check_args()
prep_folders(args)
ublast_BvE(args, usearch_path)
Euk_Contigs, Prok_Contigs, Und_Contigs = compare_hits(args)
#update_log(args, Euk_Contigs, Prok_Contigs, Und_Contigs)
clean_up(args)
next_script(args)
main()
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