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GO_Associations.py
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GO_Associations.py
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#####################################################################################################################################################################
#
# Script used in:
#
# "Gene expression profiling across ontogenetic stages in wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation."
# Luis Leal, Venkat Talla, Thomas Källman, Magne Friberg, Christer Wiklund, Vlad Dincă, Roger Vila, Niclas Backström
# Mol. Eco. (2018)
#
#
#####################################################################################################################################################################
#
# Luis Leal
# Uppsala University, Uppsala, Sweden, 2017
# Written in Python 3
#
#####################################################################################################################################################################
#####################################################################################################################################################################
#
# Script used to associate GO terms to each transcript/gene
#
#####################################################################################################################################################################
#####################################################################################################################################################################
#
#
# Input files: 1 -> Trinotate annotation report, in csv format
# 2 -> sprot_OUT_Insecta.txt file (based on uniprot_sprot_invertebrates.dat.gz (Knowledge Base) reference file, filtered for Insecta only)
# 3 -> trembl_OUT_Insecta.txt file (based on uniprot_trembl_invertebrates.dat.gz (trembl) reference file, filtered for Insecta only)
#
# Output: 1 files -> file associating each Trinity gene entry to a known gene and its associated GO terms
#
#
# Strategy:
# 1. Associate Drosophila and lepidopteran hits to GO-BioProcess terms, using UniProt-sprot db
# 2. If 1. doesn't work, use UniProt-trembl
# 3. If 1-2 don't work, just get the gene name, as well as GO-MolFunction and GO-CellComponent (as well as Pfam GO terms)
# 4. Otherwise, file Trinity gene as a new gene
#
#
#
#
###
print('\n Gleaning data ...')
######################################################### USAGE
error_message1 = ' \n \
USAGE: $python3 GO_Associations.py <trinotate_annotation_report-invertebrates.csv> <sprot_OUT_Insecta.txt> <sprot_OUT_trembl_Insecta.txt> <results_OUT.csv> \n'
######################################################### LOAD STANDARD MODULES
import sys
import re # 're' module provides regular expression matching operations
import ast # required to convert reference tree from string to list
import os # required to create new folders
import time
import csv #required to open csv file
from pdb import set_trace as bp # when using break points during debugging >> useage: bp()
######################################################## OPEN INPUT FILES
try:
trinotate_list = list() #open Trinotate output file as csv
with open(sys.argv[1], newline='') as csvfile1:
inputfile_1 = csv.reader(csvfile1, delimiter='\t')
for row in inputfile_1:
trinotate_list.append(row)
# print(', '.join(row))
except:
print('\n Error[1]: input file missing.')
print(error_message1)
exit()
try:
sprot_inv_list = list() #open sprot_OUT_invertebrates file as csv
with open(sys.argv[2], newline='') as csvfile2:
inputfile_4 = csv.reader(csvfile2, delimiter='\t')
for row in inputfile_4:
sprot_inv_list.append(row)
except:
print('\n Error[2]: input file missing.')
print(error_message1)
exit()
try:
sprot_trembl_list = list() #open trembl_OUT_invertebrates (Knowledge Base) file as csv
with open(sys.argv[3], newline='') as csvfile3:
inputfile_5 = csv.reader(csvfile3, delimiter='\t')
for row in inputfile_5:
sprot_trembl_list.append(row)
except:
print('\n Error[3]: input file missing.')
print(error_message1)
exit()
try:
outFileName_user = sys.argv[4] # read output file name
if outFileName_user == '' :
print('\n Error[4]: input file missing.')
print(error_message1)
exit()
except:
print('\n Error[4]: input file missing.')
print(error_message1)
exit()
####################################################### FUNCTION: readGENE
def readGene(geneName_long):
if geneName_long != "." :
mark_g = geneName_long.find('|')
if mark_g != -1 :
aux_g = geneName_long[(mark_g+1):]
mark_g2 = aux_g.find('|')
if mark_g2 != -1 :
geneName_long = aux_g[:mark_g2]
return geneName_long
####### END
####################################################### FUNCTION: updateList
def updateList(referenceS, newS) :
if newS == '.' or newS == '' :
aux_output = referenceS
elif referenceS == '.' or referenceS == '' :
aux_output = newS
elif newS not in referenceS :
aux_output = referenceS + "`" + newS
else:
aux_output = referenceS
return aux_output
####### END
####################################################### FUNCTION: cleanGO
def cleanGO(entry_aux) :
aux_list1 = list()
aux_list_terms = list()
if entry_aux != "." and entry_aux != "":
for m in re.finditer('GO:', entry_aux): # find all GO terms in description
aux_list1.append(m.start())
for n in range(len(aux_list1)) : # for all GO terms in description, get GO term (based on index)
GO_aux3 = entry_aux[aux_list1[n]:(aux_list1[(n)]+10)]
#print(GO_aux3)
aux_list_terms.append(GO_aux3)
aux_list_terms = sorted(list(set(aux_list_terms))) # remove duplicates and sort list of GO terms alphabetically
Go_clean = "^NA`".join(aux_list_terms) # convert list to string (Trinotate format)
else :
Go_clean = entry_aux
return Go_clean
####### END
######################################################## PROCESS DATA
## read sprot_OUT_invertebrates file
## note: each Entry_name (UniProt-KB) entry may be associated to more than one Accession code (UniProt)
sprotKB_Entry_name_list = list()
sprotKB_Accession_list = list()
sprotKB_ProteinName_list = list()
sprotKB_GeneName_list = list()
sprotKB_Organism = list()
sprotKB_KEGG_list = list()
sprotKB_FlyBase_ID_list = list()
sprotKB_GO_BioProcess_list = list()
sprotKB_GO_MolFunction_list = list()
sprotKB_GO_CelComponent_list = list()
sprotKB_Pfam_list = list()
for line in sprot_inv_list :
aux_A = line[1] # reads Accession code(s)
aux_A_list = aux_A.split(';') # gets individual Accession codes (if there is more than one)
aux_en = line[0] # reads Entry_name
aux_pn = line[2] # reads Protein Name
aux_gn = line[4] # reads Gene Name
aux_o = line[5] # reads Organism name
aux_k = line[7] # reads KEGG
aux_fb = line[8] # reads FlyBase ID
aux_goBP = line[11] # reads GO_BioProcess codes
aux_goMF = line[12] # reads GO_MolFunction codes
aux_goCC = line[13] # reads GO_CelComponent codes
aux_pf = line[14] # reads pfam code(s)
#
aux_2 = aux_gn[:5] #if there is a clear gene name, (line starts with 'Name=', get it)
if aux_2 == "Name=" :
aux_3 = aux_gn[5:]
mark_gn = aux_3.find(' ')
if mark_gn == -1 :
aux_gn = aux_3
else :
aux_gn = aux_3[:(mark_gn-1)]
#
for code in aux_A_list :
sprotKB_Accession_list.append(code)
sprotKB_Entry_name_list.append(aux_en)
sprotKB_ProteinName_list.append(aux_pn)
sprotKB_GeneName_list.append(aux_gn)
sprotKB_Organism.append(aux_o)
sprotKB_KEGG_list.append(aux_k)
sprotKB_FlyBase_ID_list.append(aux_fb)
sprotKB_GO_BioProcess_list.append(aux_goBP)
sprotKB_GO_MolFunction_list.append(aux_goMF)
sprotKB_GO_CelComponent_list.append(aux_goCC)
sprotKB_Pfam_list.append(aux_pf)
#print(aux_en, code,aux_pn,aux_gn,aux_o,aux_k,aux_fb,aux_goBP,aux_pf)
## read trembl_invertebrates file
## note: each Entry_name (UniProt-trembl) entry may be associated to more than one Accession code (UniProt)
sprot_trembl_Entry_name_list = list()
sprot_trembl_Accession_list = list()
sprot_trembl_ProteinName_list = list()
sprot_trembl_GeneName_list = list()
sprot_trembl_Organism = list()
sprot_trembl_KEGG_list = list()
sprot_trembl_FlyBase_ID_list = list()
sprot_trembl_GO_BioProcess_list = list()
sprot_trembl_GO_MolFunction_list = list()
sprot_trembl_GO_CelComponent_list = list()
sprot_trembl_Pfam_list = list()
for line in sprot_trembl_list :
aux_A = line[1] # reads Accession code(s)
aux_A_list = aux_A.split(';') # gets individual Accession codes (if there is more than one)
aux_en = line[0] # reads Entry_name
aux_pn = line[2] # reads Protein Name
aux_gn = line[4] # reads Gene Name
aux_o = line[5] # reads Organism name
aux_k = line[7] # reads KEGG
aux_fb = line[8] # reads FlyBase ID
aux_goBP = line[11] # reads GO_BioProcess codes
aux_goMF = line[12] # reads GO_MolFunction codes
aux_goCC = line[13] # reads GO_CelComponent codes
aux_pf = line[14] # reads pfam code(s)
#
aux_2 = aux_gn[:5] #if there is a clear gene name, (line starts with 'Name=', get it)
if aux_2 == "Name=" :
aux_3 = aux_gn[5:]
mark_gn = aux_3.find(' ')
if mark_gn == -1 :
aux_gn = aux_3
else :
aux_gn = aux_3[:(mark_gn-1)]
#
for code in aux_A_list :
sprot_trembl_Accession_list.append(code)
sprot_trembl_Entry_name_list.append(aux_en)
sprot_trembl_ProteinName_list.append(aux_pn)
sprot_trembl_GeneName_list.append(aux_gn)
sprot_trembl_Organism.append(aux_o)
sprot_trembl_KEGG_list.append(aux_k)
sprot_trembl_FlyBase_ID_list.append(aux_fb)
sprot_trembl_GO_BioProcess_list.append(aux_goBP)
sprot_trembl_GO_MolFunction_list.append(aux_goMF)
sprot_trembl_GO_CelComponent_list.append(aux_goCC)
sprot_trembl_Pfam_list.append(aux_pf)
#print(aux_en, code,aux_pn,aux_gn,aux_o,aux_k,aux_fb,aux_goBP,aux_pf)
### extract Trinity names ; extract associated gene names found by Trinotate; store in dictionary
Trinity_DIC = dict() # dictionary: associates each Trinity gene to a Drosophila or Lep gene (or another, if no Dro/Lep gene found)
Trinity_DIC_shadow = dict() # keeps track of gene hits not associated to GO-BioProc terms
trinity_list = list() #list of all individual Trinity genes
#org_List = ("inv","inv","Drosophila melanogaster", "Bombyx mori", "Danaus plexippus", "Papilio machaon","Drosophila melanogaster", "Bombyx mori", "Danaus plexippus", "Papilio machaon") #list of species used during BLASTX and BLASTP
flag1 = 0 #flag used to skip header
for line in trinotate_list:
#
gene_REF = "."
geneBasket_list = list() #list of hits (genes)
if flag1 == 1 :
#
trinity_name = line[0] #Trinity gene name, as listed in Trinotate
if trinity_name not in trinity_list :
trinity_list.append(trinity_name) #saves Trinity name to list
#
sprot_Top_BLASTX_hit = line[2]
if sprot_Top_BLASTX_hit != "." :
mark_g = sprot_Top_BLASTX_hit.find('^')
if mark_g != -1 :
sprot_Top_BLASTX_hit = sprot_Top_BLASTX_hit[:mark_g]
geneBasket_list.append(sprot_Top_BLASTX_hit)
#
sprot_Top_BLASTP_hit = line[6]
if sprot_Top_BLASTP_hit != "." :
mark_g = sprot_Top_BLASTP_hit.find('^')
if mark_g != -1 :
sprot_Top_BLASTP_hit = sprot_Top_BLASTP_hit[:mark_g]
geneBasket_list.append(sprot_Top_BLASTP_hit)
#
Drosophila_Uniprot_blastx_hit = line[10]
Drosophila_Uniprot_blastx_hit = readGene(Drosophila_Uniprot_blastx_hit)
geneBasket_list.append(Drosophila_Uniprot_blastx_hit)
#
Bombyx_blastx_hit = line[14]
Bombyx_blastx_hit = readGene(Bombyx_blastx_hit)
geneBasket_list.append(Bombyx_blastx_hit)
#
Danaus_blastx_hit = line[16]
Danaus_blastx_hit = readGene(Danaus_blastx_hit)
geneBasket_list.append(Danaus_blastx_hit)
#
Papilio_blastx_hit = line[18]
Papilio_blastx_hit = readGene(Papilio_blastx_hit)
geneBasket_list.append(Papilio_blastx_hit)
#
Drosophila_Uniprot_blastp_hit = line[21]
Drosophila_Uniprot_blastp_hit = readGene(Drosophila_Uniprot_blastp_hit)
geneBasket_list.append(Drosophila_Uniprot_blastp_hit)
#
Bombyx_blastp_hit = line[25]
Bombyx_blastp_hit = readGene(Bombyx_blastp_hit)
geneBasket_list.append(Bombyx_blastp_hit)
#
Danaus_blastp_hit = line[27]
Danaus_blastp_hit = readGene(Danaus_blastp_hit)
geneBasket_list.append(Danaus_blastp_hit)
#
Papilio_blastp_hit = line[29]
Papilio_blastp_hit = readGene(Papilio_blastp_hit)
geneBasket_list.append(Papilio_blastp_hit)
#
Pfam_Trinotate = line[31]
if Pfam_Trinotate != "." :
mark_g = Pfam_Trinotate.find('^')
if mark_g != -1 :
Pfam_Trinotate = Pfam_Trinotate[:mark_g]
#
Kegg_Trinotate = line[35]
gene_ontology_blast_Trinotate = line[36]
gene_ontology_pfam_Trinotate = line[37]
#
flag_GO = 0 # indicates whether GO-BioProc terms have been found for the current Trinity gene (0: no; 1: yes)
#print(trinity_name, geneBasket_list)
for k in range(len(geneBasket_list)) :
if k==0 or k==1 : continue # consider only Drosophila and Lep hits
if geneBasket_list[k] == "." : continue
if geneBasket_list[k] in sprotKB_Accession_list : # initial search done on UniProt-KB
aux_i = sprotKB_Accession_list.index(geneBasket_list[k])
hit_en = sprotKB_Entry_name_list[aux_i]
hit_pn = sprotKB_ProteinName_list[aux_i]
hit_gn = sprotKB_GeneName_list[aux_i]
hit_on = sprotKB_Organism[aux_i]
hit_kl = sprotKB_KEGG_list[aux_i]
hit_fb = sprotKB_FlyBase_ID_list[aux_i]
hit_goBP = sprotKB_GO_BioProcess_list[aux_i]
hit_goMF = sprotKB_GO_MolFunction_list[aux_i]
hit_goCC = sprotKB_GO_CelComponent_list[aux_i]
#hit_pf = sprotKB_Pfam_list[aux_i]
hit_pf = gene_ontology_pfam_Trinotate #Use Trinotate Pfam hits
if hit_goBP != '.' and hit_goBP != '' :
flag_GO = 1
if trinity_name not in Trinity_DIC :
Trinity_DIC[trinity_name] = (hit_en, geneBasket_list[k], hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "KB")
else :
aux_dic_list2 = Trinity_DIC.get(trinity_name ,0)
hit_en = updateList(aux_dic_list2[0], hit_en)
hit_ac = updateList(aux_dic_list2[1], geneBasket_list[k])
hit_pn = updateList(aux_dic_list2[2], hit_pn)
hit_gn = updateList(aux_dic_list2[3], hit_gn)
hit_on = updateList(aux_dic_list2[4], hit_on)
hit_kl = updateList(aux_dic_list2[5], hit_kl)
hit_fb = updateList(aux_dic_list2[6], hit_fb)
hit_goBP = updateList(aux_dic_list2[7], hit_goBP)
hit_goMF = updateList(aux_dic_list2[8], hit_goMF)
hit_goCC = updateList(aux_dic_list2[9], hit_goCC)
hit_pf = updateList(aux_dic_list2[10], hit_pf)
Trinity_DIC[trinity_name] = (hit_en, hit_ac, hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "KB")
else :
if flag_GO == 0 : #use shadow dictionary only if no GO terms have been found so far
if trinity_name not in Trinity_DIC_shadow :
Trinity_DIC_shadow[trinity_name] = (hit_en, geneBasket_list[k], hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "GO-BP_missing")
else :
aux_dic_list2 = Trinity_DIC_shadow.get(trinity_name ,0)
hit_en = updateList(aux_dic_list2[0], hit_en)
hit_ac = updateList(aux_dic_list2[1], geneBasket_list[k])
hit_pn = updateList(aux_dic_list2[2], hit_pn)
hit_gn = updateList(aux_dic_list2[3], hit_gn)
hit_on = updateList(aux_dic_list2[4], hit_on)
hit_kl = updateList(aux_dic_list2[5], hit_kl)
hit_fb = updateList(aux_dic_list2[6], hit_fb)
hit_goBP = updateList(aux_dic_list2[7], hit_goBP)
hit_goMF = updateList(aux_dic_list2[8], hit_goMF)
hit_goCC = updateList(aux_dic_list2[9], hit_goCC)
hit_pf = updateList(aux_dic_list2[10], hit_pf)
Trinity_DIC_shadow[trinity_name] = (hit_en, hit_ac, hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "GO-BP_missing")
#
if flag_GO == 0 : # if no GO terms have been found so far (using UniProt-KB), switch to UniProt-trembl
for k in range(len(geneBasket_list)) :
if geneBasket_list[k] in sprot_trembl_Accession_list :
aux_i = sprot_trembl_Accession_list.index(geneBasket_list[k])
hit_en = sprot_trembl_Entry_name_list[aux_i]
hit_pn = sprot_trembl_ProteinName_list[aux_i]
hit_gn = sprot_trembl_GeneName_list[aux_i]
hit_on = sprot_trembl_Organism[aux_i]
hit_kl = sprot_trembl_KEGG_list[aux_i]
hit_fb = sprot_trembl_FlyBase_ID_list[aux_i]
hit_goBP = sprot_trembl_GO_BioProcess_list[aux_i]
hit_goMF = sprot_trembl_GO_MolFunction_list[aux_i]
hit_goCC = sprot_trembl_GO_CelComponent_list[aux_i]
#hit_pf = sprotKB_Pfam_list[aux_i]
hit_pf = gene_ontology_pfam_Trinotate #Use Trinotate Pfam hits
#print(trinity_name,geneBasket_list[k],hit_goBP)
if hit_goBP != '.' and hit_goBP != '' :
flag_GO = 1
if trinity_name not in Trinity_DIC :
Trinity_DIC[trinity_name] = (hit_en, geneBasket_list[k], hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "trembl")
else :
aux_dic_list2 = Trinity_DIC.get(trinity_name ,0)
hit_en = updateList(aux_dic_list2[0], hit_en)
hit_ac = updateList(aux_dic_list2[1], geneBasket_list[k])
hit_pn = updateList(aux_dic_list2[2], hit_pn)
hit_gn = updateList(aux_dic_list2[3], hit_gn)
hit_on = updateList(aux_dic_list2[4], hit_on)
hit_kl = updateList(aux_dic_list2[5], hit_kl)
hit_fb = updateList(aux_dic_list2[6], hit_fb)
hit_goBP = updateList(aux_dic_list2[7], hit_goBP)
hit_goMF = updateList(aux_dic_list2[8], hit_goMF)
hit_goCC = updateList(aux_dic_list2[9], hit_goCC)
hit_pf = updateList(aux_dic_list2[10], hit_pf)
Trinity_DIC[trinity_name] = (hit_en, hit_ac, hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "trembl")
else :
if flag_GO == 0 : #use shadow dictionary only if no GO terms have been found so far
if trinity_name not in Trinity_DIC_shadow :
Trinity_DIC_shadow[trinity_name] = (hit_en, geneBasket_list[k], hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "trembl_GO-BP_missing")
else :
aux_dic_list2 = Trinity_DIC_shadow.get(trinity_name ,0)
hit_en = updateList(aux_dic_list2[0], hit_en)
hit_ac = updateList(aux_dic_list2[1], geneBasket_list[k])
hit_pn = updateList(aux_dic_list2[2], hit_pn)
hit_gn = updateList(aux_dic_list2[3], hit_gn)
hit_on = updateList(aux_dic_list2[4], hit_on)
hit_kl = updateList(aux_dic_list2[5], hit_kl)
hit_fb = updateList(aux_dic_list2[6], hit_fb)
hit_goBP = updateList(aux_dic_list2[7], hit_goBP)
hit_goMF = updateList(aux_dic_list2[8], hit_goMF)
hit_goCC = updateList(aux_dic_list2[9], hit_goCC)
hit_pf = updateList(aux_dic_list2[10], hit_pf)
Trinity_DIC_shadow[trinity_name] = (hit_en, hit_ac, hit_pn, hit_gn, hit_on, hit_kl, hit_fb, hit_goBP, hit_goMF, hit_goCC, hit_pf, "trembl_GO-BP_missing")
else :
flag1 = 1
##### Consolidate dictionaries
for gene in trinity_list:
if gene not in Trinity_DIC :
Trinity_DIC[gene] = Trinity_DIC_shadow.get(gene ,0)
### remove duplicate GO entries from Trinity_DIC dictionary
for gene in trinity_list :
entry_aux_list = Trinity_DIC.get(gene ,0)
if type(entry_aux_list) == tuple : entry_aux_list = list(entry_aux_list) #converts tuple to list
if entry_aux_list != "0" and entry_aux_list != 0:
#
entry_goBP = entry_aux_list[7] ##GO-BP
new_goBP = cleanGO(entry_goBP)
#
entry_goMF = entry_aux_list[8] ##GO-MF
new_goMF = cleanGO(entry_goMF)
#
entry_goCC = entry_aux_list[9] ##GO-CC
new_goCC = cleanGO(entry_goCC)
#
entry_gopfam = entry_aux_list[10] ##GO-Pfam
new_gopfam = cleanGO(entry_gopfam)
#
allGo = new_goBP + "^NA`" + new_goMF + "^NA`" + new_goCC + "^NA`" + new_gopfam ## All GO terms
new_allGo = cleanGO(allGo)
#
entry_aux_list.append(new_goBP)
entry_aux_list.append(new_goMF)
entry_aux_list.append(new_goCC)
entry_aux_list.append(new_gopfam)
entry_aux_list.append(new_allGo)
#
Trinity_DIC[gene] = entry_aux_list # new columns containing clean GO terms add to each entry
#print dictionaries
#for gene in trinity_list:
# aux_dic_list2 = Trinity_DIC.get(gene ,0)
# print()
# print(gene, aux_dic_list2)
######################################################## SAVE RESULTS TO FILE
outFileName1 = outFileName_user
outfile1 = open(outFileName1, 'w')
aux_save = '"Trinity_gene_ID"' + '\t' + '"Entry_name"' + '\t' + '"Accession_code"' + '\t' + '"Protein_name"' + '\t' + '"Gene_name"' + '\t' + '"Organism_name"' + '\t' + '"KEGG"' + '\t' + '"FlyBase"' + '\t' + '"GO_BioProcess"' + '\t' + '"GO_MolFunction"' + '\t' + '"GO_CelComponent"' + '\t' + '"GO_Pfam"' + '\t' + '"KB_or_trembl"' + '\t' + '"GO_BioProcess_clean"' + '\t' + '"GO_MolFunction_clean"' + '\t' + '"GO_CelComponent_clean"' + '\t' + '"GO_Pfam_clean"' + '\t' + '"All_GO_terms_clean"' + '\n' #write header
outfile1.write(aux_save)
for gene in trinity_list :
entry_aux_list = Trinity_DIC.get(gene ,0)
#print('\n', entry_aux_list)
if entry_aux_list != "" and entry_aux_list != "." and entry_aux_list != 0 :
aux_save = '"' + gene + '"'
for k in range(len(entry_aux_list)) :
#print(entry_aux_list[k])
if entry_aux_list[k] == '' : entry_aux_list[k] = '.'
aux_save = aux_save + '\t' + '"' + entry_aux_list[k] + '"'
else :
aux_save = '"' + gene + '"'
for k in range(0,17) :
aux_save = aux_save + '\t' + '"."'
aux_save = aux_save + '\n'
outfile1.write(aux_save)
outfile1.close()
print()
print('\n Done!')