mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 06:50:24 +08:00
373 lines
15 KiB
Python
373 lines
15 KiB
Python
#!/usr/bin/env python3.5
|
|
|
|
##__Updated__: 16_10_2017
|
|
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
|
|
##__Usage__: python 3_CountOGsDiamond.py --help
|
|
|
|
|
|
##########################################################################################
|
|
## This script is intended to classify the STRONGLY Eukaryotic and UNDETERMINED/UNKNOWN ##
|
|
## contigs into different OGs (e.g. orthologous gene-families) ##
|
|
## ##
|
|
## For more info about the OGs, check out: OrthoMCL.org ##
|
|
## ##
|
|
## Prior to running this script, ensure the following: ##
|
|
## ##
|
|
## 1. You have assembled your transcriptome and COPIED the 'assembly' file ##
|
|
## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ##
|
|
## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ##
|
|
## 3. Removed SSU/LSU sequences from your Fasta File ##
|
|
## ##
|
|
## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
|
|
## ##
|
|
## Next Script(s) to Run: ##
|
|
## 4_StopFrequency.py ##
|
|
## ##
|
|
##########################################################################################
|
|
|
|
import argparse, os, sys, re
|
|
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+' "usearch" '+color.END+color.BOLD+'executable.\n\n'+color.END)
|
|
print (color.BOLD+color.BLUE+'LOOK FOR:\n\n'+color.RED\
|
|
+'#------------------------------ UPDATE USEARCH 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 + '\n\nThis script will categorize Contigs into'+color.ORANGE+' "Homologous" '\
|
|
+color.END+color.BOLD+'Gene Families (OGs)\nbased on '+color.RED+'OrthoMCL'+color.END\
|
|
+color.BOLD+"'s Gene Family Grouping\n\n\nNotes on this script and "+color.GREEN+\
|
|
'OrthoMCL Families'+color.END+color.BOLD+' can be found\nat the bottom of '+color.GREEN\
|
|
+'THIS script (3_CountOGsDiamond.py)\n'+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 enriched \nwith'\
|
|
' Eukaryotic protein coding transcripts'+color.END)
|
|
required_arg_group.add_argument('--databases','-g', action='store',
|
|
help=color.BOLD+color.GREEN+"Path to fasta file with Hook sequences"+color.END)
|
|
|
|
optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
|
|
optional_arg_group.add_argument('--threads','-t', default='2',
|
|
help=color.BOLD+color.GREEN+' Number of threads to use for BLAST\n (default = 2)\n'+color.END)
|
|
optional_arg_group.add_argument('--evalue','-e', default=1e-5, type = float,
|
|
help=color.BOLD+color.GREEN+' Maximum e-value for OG assignment\n (default = 1e-5)\n'+color.END)
|
|
optional_arg_group.add_argument('-author', action='store_true',
|
|
help=color.BOLD+color.GREEN+' Prints 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 3_CountOGsDiamond.py'\
|
|
' --input_file ../Op_me_Xxma/Op_me_Xxma_WTA_NBU.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
|
|
|
|
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('WTA_EPU.fasta') != True:
|
|
print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\
|
|
' with '+color.GREEN+'2b_remove_Bact.py '+color.END+color.BOLD+'are valid\n\n'\
|
|
'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\
|
|
'"WTA_NBU.fasta"\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_OG') != True:
|
|
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
|
|
+color.ORANGE+'db_OG 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\n\n.'+color.END)
|
|
valid_arg += 1
|
|
|
|
ogdb_count = 0
|
|
for file in os.listdir(args.databases + '/db_OG'):
|
|
if file.endswith('.dmnd'):
|
|
ogdb_count += 1
|
|
|
|
if ogdb_count == 0:
|
|
print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
|
|
'Diamond formatted '+color.ORANGE+'Gene Family databases!\n\n'+color.END+color.BOLD+\
|
|
'Ensure that they can be found in the '+color.ORANGE+'db_OG 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.\n\n'+color.END)
|
|
valid_arg += 1
|
|
elif ogdb_count > 1:
|
|
print('\nMultiple OG databases found. Please only provide 1 database in the db_OG folder.\n')
|
|
valid_arg += 1
|
|
|
|
return valid_arg
|
|
|
|
|
|
###########################################################################################
|
|
###--------------------------- Does the Inital Folder Prep -----------------------------###
|
|
###########################################################################################
|
|
|
|
def prep_folders(args):
|
|
|
|
OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/'
|
|
|
|
if os.path.isdir(OG_folder) != True:
|
|
os.system('mkdir '+OG_folder)
|
|
|
|
|
|
###########################################################################################
|
|
###--------------------- Runs Diamond on Split OrthoMCL Databases ----------------------###
|
|
###########################################################################################
|
|
|
|
def OG_diamond(args, diamond_path):
|
|
|
|
print (color.BOLD+'\nStarting to "BLAST" against OG databases'+color.END)
|
|
|
|
OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/'
|
|
db = [file for file in os.listdir(args.databases + '/db_OG') if file.endswith('.dmnd')][0]
|
|
|
|
print (color.BOLD + '\n\n"BLAST"-ing against OG database using DIAMOND: ' + color.DARKCYAN + db + color.END + '\n\n')
|
|
|
|
OG_diamond_cmd = diamond_path + ' blastx -q ' + args.input_file + ' -d ' + args.databases + '/db_OG/' + db + ' --evalue ' + str(args.evalue) + ' --threads 60 --subject-cover 0.35 --outfmt 6 -o ' + OG_folder + 'allOGresults.tsv'
|
|
|
|
os.system(OG_diamond_cmd)
|
|
|
|
|
|
###########################################################################################
|
|
###--------------- Keeps the Single BEST Hit (HSP-score) Per Transcript ----------------###
|
|
###########################################################################################
|
|
|
|
def keep_best(args):
|
|
|
|
print (color.BOLD+color.PURPLE+'\n\nProcessing OG-database results to keep only the BEST match for each transcript\n\n'+color.END)
|
|
|
|
OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/'
|
|
|
|
inTSV = [i for i in open(OG_folder + 'allOGresults.tsv').readlines()]
|
|
|
|
inTSV.sort(key = lambda x: -float(x.split('\t')[-1]))
|
|
|
|
keep = []
|
|
for i in inTSV:
|
|
if any(i.split('\t')[0] in j for j in keep) != True:
|
|
keep.append(i)
|
|
|
|
updated_lines = list(set([line.split('\t')[0]+'_'+'_'.join(line.split('\t')[1].split('_')[-2:])+'\t'+'\t'.join(line.split('\t')[1:]) for line in keep]))
|
|
|
|
with open(args.input_file.replace('.fasta','.Renamed_allOGCleanresults.tsv'), 'w+') as w:
|
|
for i in updated_lines:
|
|
w.write(i)
|
|
|
|
|
|
###########################################################################################
|
|
###-------- Copies and Updates Names of Transcripts With OG Hits to New Fasta ----------###
|
|
###########################################################################################
|
|
|
|
def update_fasta(args):
|
|
|
|
print (color.BOLD+color.PURPLE+'Updating Fasta File Sequence Names with their BEST OG hits\n\n'+color.END)
|
|
|
|
Renamed_TSV = args.input_file.replace('.fasta','.Renamed_allOGCleanresults.tsv')
|
|
|
|
keep = [i for i in open(Renamed_TSV).readlines() if i != '\n']
|
|
|
|
keep_dict = { }
|
|
for line in keep:
|
|
try:
|
|
og_number = re.split('OG.{1}_', line.split('\t')[1])[1][:6]
|
|
og_prefix = line.split('\t')[1].split(og_number)[0][-4:]
|
|
og = og_prefix + og_number
|
|
|
|
keep_dict.update({ re.split('_OG.{1}_', line.split('\t')[0])[0] : re.split('_OG.{1}_', line.split('\t')[0])[0] + '_' + og_prefix + line.split('\t')[1].split('_')[-1] })
|
|
except IndexError:
|
|
pass
|
|
|
|
inFasta = [i for i in SeqIO.parse(args.input_file,'fasta')]
|
|
|
|
updated_seq_name = ['>'+keep_dict[i.description]+'\n'+str(i.seq)+'\n' for i in inFasta if i.description in keep_dict.keys()]
|
|
|
|
seqs_without_OG = ['>'+i.description+'\n'+str(i.seq)+'\n' for i in inFasta if i.description not in keep_dict.keys()]
|
|
|
|
with open(args.input_file.replace('.fasta','.Renamed.fasta'),'w+') as w:
|
|
for i in updated_seq_name:
|
|
w.write(i)
|
|
|
|
with open(args.input_file.replace('.fasta','.LackOG.fasta'),'w+') as x:
|
|
for i in seqs_without_OG:
|
|
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 -------------------###
|
|
##########################################################################################
|
|
|
|
def clean_up(args):
|
|
|
|
OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/'
|
|
|
|
os.system('rm ' + args.input_file)
|
|
|
|
os.system('cp ' + args.input_file.replace('.fasta','.Renamed.fasta') + ' ' + OG_folder)
|
|
|
|
os.system('cp ' + args.input_file.replace('.fasta','.Renamed_allOGCleanresults.tsv') + ' ' + OG_folder)
|
|
|
|
|
|
###########################################################################################
|
|
###-------------------------------- Next Script Message --------------------------------###
|
|
###########################################################################################
|
|
|
|
def next_script(args):
|
|
|
|
home_folder = '../'+args.input_file.split('/')[1]+'/'
|
|
|
|
print (color.BOLD+'\nLook for '+color.DARKCYAN+args.input_file.split('/')[-1]\
|
|
.replace('.fasta','WTA_EPU.fasta')+color.END+color.BOLD+' in the '+home_folder\
|
|
+' Folder\n\n' + color.END)
|
|
|
|
print (color.BOLD+'Next Script is: '+color.GREEN+'4_InFrameStopFreq.py\n\n'+ color.END)
|
|
|
|
|
|
##########################################################################################
|
|
###--------------- Checks Command Line Arguments and Calls on Functions ---------------###
|
|
##########################################################################################
|
|
|
|
def main():
|
|
|
|
usearch_path = check_diamond_path()
|
|
|
|
args = check_args()
|
|
|
|
prep_folders(args)
|
|
|
|
OG_diamond(args, usearch_path)
|
|
|
|
keep_best(args)
|
|
|
|
update_fasta(args)
|
|
|
|
#update_log(args)
|
|
|
|
clean_up(args)
|
|
|
|
next_script(args)
|
|
|
|
main()
|