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omicR.py
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omicR.py
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import tkinter as tk
from tkinter import *
from tkinter import filedialog
from tkinter import messagebox
from Bio import Entrez
import os
doubleBackSlash = r'/ '[0]
class Script1:
def __init__(self):
self.a_InputCSVFileName = ""
self.b_OutputPATH = ""
self.c_OutputFileName = "your_original_file"
self.d_Row_Where_header_starts = 0
self.e_rowWhereDataStarts = 0
self.f_SEQUENCE_COLUMN = 0
#self.g_AVG_READS = 0
#self.i_Nbases = 0
def Add_terminal_path_slash(self, path):
path_with_slash = path + "\\"
# assert isinstance(path_with_slash, object)
return path_with_slash
def main(self):
# make variables
index = 1
index_2 = 1
Output_path_and_name = self.b_OutputPATH + self.c_OutputFileName + ".fasta"
Output_extra_file = self.b_OutputPATH + self.c_OutputFileName + "_InputFile_with_unique_ID.txt"
inputFile = open(self.a_InputCSVFileName, errors='ignore')
OutputFile = open(Output_path_and_name, 'w')
Output_EXTRA = open(Output_extra_file, 'w')
# MAKING FASTA FILE
# Read through and skip header row
for c in range(0, self.d_Row_Where_header_starts):
HeaderTemp = inputFile.readline()
# Reading through the rows and breaking at the end of the data
tempstring = "temp"
while tempstring:
tempstring = inputFile.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split(",")
#SeqID = rowlist[self.g_AVG_READS]
TrimmedSequence = rowlist[self.f_SEQUENCE_COLUMN]
#NBases = rowlist[self.i_Nbases]
OutputRows = ">" + str(index) + '\n' + TrimmedSequence + '\n'
#OutputRows = ">" + str(index) + "_" + SeqID + "_" + NBases + '\n' + TrimmedSequence + '\n'
index += 1
OutputFile.write(OutputRows)
inputFile.close()
OutputFile.close()
# MAKING INPUT FILE FOR FILTERING AFTER BLAST
# READ AND WRITE AGAIN THE INPUT FILE FOR THIS SCRIPT
# Original File
# Reading and writing headers
inputFile_2 = open(self.a_InputCSVFileName, errors='ignore')
AllHeadersJoined_inputFile_2 = ""
for c in range(0, self.d_Row_Where_header_starts):
headerTemp = inputFile_2.readline()
headerLine = headerTemp.splitlines()
y = headerLine[0]
headerList = y.split(",")
header_tab_delimited = ""
for j in range(0, (len(headerList) - 1)):
header_tab_delimited += headerList[j] + '\t'
header_tab_delimited += headerList[(len(headerList) - 1)]
AllHeadersJoined_inputFile_2 += ("FastaFileID" + '\t' + header_tab_delimited + '\n') # headerList[f_SEQUENCE_COLUMN]
Output_EXTRA.write(AllHeadersJoined_inputFile_2)
# Original File
# Reading through the rows and breaking at the end of the data. Writing it into a
# new document and adding an extra column as Fasta File ID.
tempstring = "temp"
while tempstring:
tempstring = inputFile_2.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split(",")
data_tab_delimited = ""
for i in range(0, (len(rowlist) - 1)):
data_tab_delimited += rowlist[i] + '\t'
data_tab_delimited += rowlist[(len(rowlist) - 1)]
# SequenceID = rowlist[f_SEQUENCE_COLUMN]
FastaFileID = (str(index_2))
index_2 += 1
data = (FastaFileID + '\t' + data_tab_delimited + '\n')
Output_EXTRA.write(data)
inputFile_2.close()
Output_EXTRA.close()
class Script2:
def __init__(self):
self.email_DG = ""
self.genomeAccessions_DG = ""
self.OutputFilePath_DG = ""
self.fileName_DG = ""
def main(self):
# make variables
Entrez.email = self.email_DG
def get_sequences_from_ID_list_line_by_line(ids):
print(ids)
DirectoryPath = self.OutputFilePath_DG + self.fileName_DG
if not os.path.exists(DirectoryPath):
os.makedirs(DirectoryPath)
NameOfMyFile = DirectoryPath + '/' + self.fileName_DG + ".fasta"
file_DG = open(NameOfMyFile, 'w')
counter = 1
for seq_id in ids:
handle = Entrez.efetch(db="nucleotide", id=seq_id, rettype="fasta", retmode="text")
# Read Data
AllLines = handle.readlines()
# PRINT AND WRITE LANE 0
NameOfGenome_Line0 = AllLines[0].splitlines()
print(NameOfGenome_Line0)
str0 = ''.join(NameOfGenome_Line0)
file_DG.write(str0)
file_DG.write('\n')
# Create a loop to read all rows in a file
genome_without_header = AllLines[1:]
listLength = len(genome_without_header)
# print(listLength)
complete_genome_string = ""
for x in range(0, listLength):
tempList = genome_without_header[x].splitlines()
tempString = tempList[0]
complete_genome_string += tempString
file_DG.write(complete_genome_string)
file_DG.write('\n')
print(counter)
counter += 1
file_DG.close()
list_of_accessions = self.genomeAccessions_DG.split(',')
get_sequences_from_ID_list_line_by_line(list_of_accessions)
class Script3:
def __init__(self):
self.Path_To_NCBI_BLAST_Bin_Directory = ""
self.Path_To_Database_Fasta_File = ""
self.Data_Base_Type = ""
def main(self):
# CREATE DATABASE FOR RUNNING BLAST IN WINDOWS
CreateDataBase = self.Path_To_NCBI_BLAST_Bin_Directory + "makeblastdb -in " + self.Path_To_Database_Fasta_File + " -dbtype " + self.Data_Base_Type
print(CreateDataBase)
os.system(CreateDataBase)
class Script4:
def __init__(self):
self.x_Path_to_NCBI_Directory_BF = ""
self.y_DC_MegaBlast_BF = 0
self.a_Data_Base_fasta = ""
self.b_Query_fasta_file = ""
self.c_Output_Path_ = ""
# BLAST PARAMETERS
self.d_Output_file_name = "_BLAST"
self.e_word_size = "20"
self.f_Percentage_identity = "70"
self.g_number_of_threads = "4"
self.i_OutputFormat = "6"
# FIlTERING PARAMETERS
self.j_Percentage_overlap = "0.8"
self.k_bitscore = "50"
self.l_InputFile_with_unique_ID = ""
def main(self):
# make variables
Task_megaBlast = ""
if self.y_DC_MegaBlast_BF == 1:
Task_megaBlast = " -task dc-megablast "
print(Task_megaBlast)
CommandLine_BF = (self.x_Path_to_NCBI_Directory_BF + "blastn " + Task_megaBlast
+ " -db " + self.a_Data_Base_fasta + " -query "
+ self.b_Query_fasta_file + " -out " + self.c_Output_Path_ + self.d_Output_file_name + "BLAST.txt"
+ " -word_size " + self.e_word_size + " -perc_identity " + self.f_Percentage_identity
+ " -num_threads " + self.g_number_of_threads + " -outfmt " + '"' + self.i_OutputFormat +
' qseqid sacc stitle qseq sseq nident mismatch pident length evalue bitscore qstart qend sstart send gapopen gaps qlen slen"')
print(CommandLine_BF)
os.system(CommandLine_BF)
###################################################################################################################################
#####################################################PART 2
# FILTERING BLAST OUTPUTFILE
# BLAST FILTERING PARAMETRES
qseqid = 0
sacc = 1
stitle = 2
qseq = 3
sseq = 4
nident = 5
mismatch = 6
pident = 7
length = 8
evalue = 9
bitscore = 10
qstart = 11
qend = 12
sstart = 13
send = 14
gapopen = 15
gaps = 16
qlen = 17
slen = 18
PercentageOverlapINT = 19
BLAST_OUTPUT_FILE_BF = self.c_Output_Path_ + self.d_Output_file_name + "BLAST.txt"
file_BF = open(BLAST_OUTPUT_FILE_BF, 'r')
filtered_file_BF = self.c_Output_Path_ + self.d_Output_file_name + "_filtered.txt"
filtered_files_BF = open(filtered_file_BF, "w+")
# headers
AllHeadersFromFilteredFile_BF = ""
AllHeadersFromFilteredFile_BF = ("qseqid" + '\t' + "sacc" + '\t' + "stitle" + '\t' +
"qseq" + '\t' + "sseq" + '\t' + "nident" + '\t' + "mismatch" + '\t' +
"pident" + '\t' + "length" + '\t' + "evalue" + '\t' +
"bitscore" + '\t' + "qstart" + '\t' + "qend" + '\t' + "sstart" + '\t' +
"send" + '\t' + "gapopen" + '\t' + "gaps" + '\t' +
"qlen" + '\t' + "slen" + '\t' + "PercentageOverlap" + '\n')
filtered_files_BF.write(AllHeadersFromFilteredFile_BF)
# Reading files
tempstring = "temp"
while tempstring:
tempstring = file_BF.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split('\t')
columns = (rowlist[qseqid] + '\t' + rowlist[sacc] + '\t' + rowlist[stitle] + '\t' +
rowlist[qseq] + '\t' + rowlist[sseq] + '\t' + rowlist[nident] + '\t' + rowlist[mismatch] + '\t' +
rowlist[pident] + '\t' + rowlist[length] + '\t' + rowlist[evalue] + '\t' +
rowlist[bitscore] + '\t' + rowlist[qstart] + '\t' + rowlist[qend] + '\t' + rowlist[
sstart] + '\t' +
rowlist[send] + '\t' + rowlist[gapopen] + '\t' + rowlist[gaps] + '\t' +
rowlist[qlen] + '\t' + rowlist[slen] + '\t')
Querylength_BF = int(rowlist[qlen])
Length_BF = int(rowlist[length])
SubjectLength_BF = int(rowlist[slen])
min_length_BF = min(Querylength_BF, SubjectLength_BF)
PercentageOverlap = (Length_BF / min_length_BF)
rowlist.append(str(PercentageOverlap))
columns = (rowlist[qseqid] + '\t' + rowlist[sacc] + '\t' + rowlist[stitle] + '\t' +
rowlist[qseq] + '\t' + rowlist[sseq] + '\t' + rowlist[nident] + '\t' + rowlist[mismatch] + '\t' +
rowlist[pident] + '\t' + rowlist[length] + '\t' + rowlist[evalue] + '\t' +
rowlist[bitscore] + '\t' + rowlist[qstart] + '\t' + rowlist[qend] + '\t' + rowlist[
sstart] + '\t' +
rowlist[send] + '\t' + rowlist[gapopen] + '\t' + rowlist[gaps] + '\t' +
rowlist[qlen] + '\t' + rowlist[slen] + '\t' + rowlist[PercentageOverlapINT] + '\n')
# FILTERING STEP 1 <<<<< DEFAULT "Percentage overlap >80% or 0.8" >>>>> AND <<<<< DEFAULT "BitScore >50" >>>>>
# HANDLES
if float(rowlist[PercentageOverlapINT]) >= float(self.j_Percentage_overlap):
if float(rowlist[bitscore]) >= int(self.k_bitscore):
filtered_files_BF.write(columns)
file_BF.close()
filtered_files_BF.close()
# TO BE CHECKED
filtered_files_2_BF = open(filtered_file_BF, 'r')
###################################################################################################################################
#####################################################PART 3
# FILTERING STEP 2
filter_part2_path_and_name_BF = self.c_Output_Path_ + self.d_Output_file_name + "_sorted.txt"
# print(filter_part2_path_and_name)
filtered_files_part2_BF = open(filter_part2_path_and_name_BF, "w")
# headers
AllHeadersFromFilteredFile = ""
AllHeadersFromFilteredFile_BF = ("qseqid" + '\t' + "sacc" + '\t' + "stitle" + '\t' +
"qseq" + '\t' + "sseq" + '\t' + "nident" + '\t' + "mismatch" + '\t' +
"pident" + '\t' + "length" + '\t' + "evalue" + '\t' +
"bitscore" + '\t' + "qstart" + '\t' + "qend" + '\t' + "sstart" + '\t' +
"send" + '\t' + "gapopen" + '\t' + "gaps" + '\t' +
"qlen" + '\t' + "slen" + '\t' + "PercentageOverlap" + '\n')
filtered_files_part2_BF.write(AllHeadersFromFilteredFile_BF)
# Reading files
lst_lst = []
counter = 0
tempstring = "temp"
while tempstring:
tempstring = filtered_files_2_BF.readline()
if tempstring == "":
break
if counter != 0:
templine = tempstring.splitlines()
x = templine[0]
rowlist_2 = x.split('\t')
lst_lst.append(rowlist_2)
columns = (rowlist_2[qseqid] + '\t' + rowlist_2[sacc] + '\t' + rowlist_2[stitle] + '\t' +
rowlist_2[qseq] + '\t' + rowlist_2[sseq] + '\t' + rowlist_2[nident] + '\t' + rowlist_2[
mismatch] + '\t' +
rowlist_2[pident] + '\t' + rowlist_2[length] + '\t' + rowlist_2[evalue] + '\t' +
rowlist_2[bitscore] + '\t' + rowlist_2[qstart] + '\t' + rowlist_2[qend] + '\t' + rowlist_2[
sstart] + '\t' +
rowlist_2[send] + '\t' + rowlist_2[gapopen] + '\t' + rowlist_2[gaps] + '\t' +
rowlist_2[qlen] + '\t' + rowlist_2[slen] + '\t' + rowlist_2[PercentageOverlapINT] + '\n')
counter += 1
# READ THE NEW FILE AND ENTER THE LOOP
# SORTING
list.sort(lst_lst, key=lambda DataRow_0: float(DataRow_0[pident]), reverse=True)
list.sort(lst_lst, key=lambda DataRow_2: float(DataRow_2[PercentageOverlapINT]), reverse=True)
list.sort(lst_lst, key=lambda DataRow_1: float(DataRow_1[bitscore]), reverse=True)
list.sort(lst_lst, key=lambda DataRow_3: DataRow_3[qseqid])
Dictionary_lst_lst = {}
# Reading list_list
length = len(lst_lst)
for i in range(length):
temp_rowlist = lst_lst[i]
temp_rowlist_length = len(temp_rowlist)
if temp_rowlist_length != 20:
print("length of tem_row_list_is:")
print(temp_rowlist_length)
continue
row_string_for_output = ""
Variable_QSeqID = temp_rowlist[qseqid]
try:
for j in range(temp_rowlist_length - 1):
temp_string = temp_rowlist[j]
row_string_for_output += (temp_string + "\t")
row_string_for_output += temp_rowlist[temp_rowlist_length - 1]
row_string_for_output += "\n"
except IndexError:
print("Exception thrown")
print(row_string_for_output)
# Tuple
TheTuple_rowlist = (Variable_QSeqID, row_string_for_output)
if Variable_QSeqID in Dictionary_lst_lst:
print("key already in dictionary")
else:
Dictionary_lst_lst[Variable_QSeqID] = row_string_for_output
filtered_files_part2_BF.write(row_string_for_output)
filtered_files_part2_BF.close()
filtered_files_2_BF.close()
###################################################################################################################################
#####################################################PART 4
###Writting_BLAST_results_back_into_original_file
Output_extra_file_BF = self.l_InputFile_with_unique_ID
Output_file_only_sequences_with_hits_BF = self.c_Output_Path_ + self.d_Output_file_name + "_only_sequences_with_hits.txt"
Output_final_BLAST_File_BF = self.c_Output_Path_ + self.d_Output_file_name + "_all_sequences_with_and_without_hits.txt"
OutputFile_BF = open(Output_final_BLAST_File_BF, 'w')
inputFilteredBLAST_File_BF = open(filter_part2_path_and_name_BF, 'r')
# INDEX
qseqid = 0
sacc = 1
stitle = 2
qseq = 3
sseq = 4
nident = 5
mismatch = 6
pident = 7
length = 8
evalue = 9
bitscore = 10
qstart = 11
qend = 12
sstart = 13
send = 14
gapopen = 15
gaps = 16
qlen = 17
slen = 18
PercentageOverlapINT = 19
# Reading files LISTS
lst_lst = []
counter = 0
header_temp = ""
Complete_output = ""
tempstring = "temp"
while tempstring:
tempstring = inputFilteredBLAST_File_BF.readline()
if counter == 0:
Split_list = tempstring.splitlines()
header_temp = Split_list[0]
if tempstring == "":
break
if counter != 0:
templine = tempstring.splitlines()
x = templine[0]
rowlist_2 = x.split('\t')
lst_lst.append(rowlist_2)
columns = (rowlist_2[qseqid] + '\t' + rowlist_2[sacc] + '\t' + rowlist_2[stitle] + '\t' +
rowlist_2[qseq] + '\t' + rowlist_2[sseq] + '\t' + rowlist_2[nident] + '\t' + rowlist_2[
mismatch] + '\t' +
rowlist_2[pident] + '\t' + rowlist_2[length] + '\t' + rowlist_2[evalue] + '\t' +
rowlist_2[bitscore] + '\t' + rowlist_2[qstart] + '\t' + rowlist_2[qend] + '\t' + rowlist_2[
sstart] + '\t' +
rowlist_2[send] + '\t' + rowlist_2[gapopen] + '\t' + rowlist_2[gaps] + '\t' +
rowlist_2[qlen] + '\t' + rowlist_2[slen] + '\t' + rowlist_2[PercentageOverlapINT] + '\n')
counter += 1
Dictionary_lst_lst = {}
# Reading list_list
length = len(lst_lst)
for i in range(length):
temp_rowlist = lst_lst[i]
temp_rowlist_length = len(temp_rowlist)
if temp_rowlist_length != 20:
continue
row_string_for_output = ""
Variable_QSeqID = temp_rowlist[qseqid]
try:
for j in range(temp_rowlist_length):
temp_string = temp_rowlist[j]
row_string_for_output += (temp_string + "\t")
row_string_for_output += "\n"
except IndexError:
print("Exception thrown")
# Tuple
TheTuple_rowlist = (Variable_QSeqID, row_string_for_output)
if Variable_QSeqID in Dictionary_lst_lst:
print("key already in dictionary")
else:
Dictionary_lst_lst[Variable_QSeqID] = row_string_for_output
print(row_string_for_output)
# OPEN THE ORIGINAL MODIFIED FILE
Original_Modified_file_BF = open(Output_extra_file_BF, 'r')
Only_sequences_with_hits_file_BF = open(Output_file_only_sequences_with_hits_BF, 'w')
counter2 = 0
Header_Temp_2 = ""
tempstring = "temp"
while tempstring:
tempstring = Original_Modified_file_BF.readline()
if counter2 == 0:
Split_list_2 = tempstring.splitlines()
Header_Temp_2 = Split_list_2[0]
OutputFile_BF.write(Header_Temp_2 + "\t" + header_temp + "\n")
Only_sequences_with_hits_file_BF.write(Header_Temp_2 + "\t" + header_temp + "\n")
if tempstring == "":
break
if counter2 != 0:
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split('\t')
Temp_QSeqID = rowlist[0]
if Temp_QSeqID in Dictionary_lst_lst:
Corresponding_row = Dictionary_lst_lst.get(Temp_QSeqID)
OutputFile_BF.write(x + "\t")
OutputFile_BF.write(Corresponding_row)
Only_sequences_with_hits_file_BF.write(x + "\t")
Only_sequences_with_hits_file_BF.write(Corresponding_row)
else:
OutputFile_BF.write(
x + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\t" + "\n")
# print("not found in dictionary")
counter2 += 1
OutputFile_BF.write(Complete_output)
Original_Modified_file_BF.close()
OutputFile_BF.close()
inputFilteredBLAST_File_BF.close()
Only_sequences_with_hits_file_BF.close()
Only_sequences_with_hits_file_BF.close()
class Script55:
def __init__(self):
self.a_BLAST_input_path_and_file_ = ""
self.b_Output_Path_ = ""
self.c_Output_file_name = "_BLAST"
# FIlTERING PARAMETERS
self.d_Percentage_overlap = "0.8"
self.e_bitscore = "50"
def main(self):
# BLAST FILTERING PARAMETERS
qseqid = 0
sacc = 1
stitle = 2
qseq = 3
sseq = 4
nident = 5
mismatch = 6
pident = 7
length = 8
evalue = 9
bitscore = 10
qstart = 11
qend = 12
sstart = 13
send = 14
gapopen = 15
gaps = 16
qlen = 17
slen = 18
PercentageOverlapINT = 19
BLAST_OUTPUT_FILE_F = self.a_BLAST_input_path_and_file_
file_F = open(BLAST_OUTPUT_FILE_F, 'r')
filtered_file_F = self.b_Output_Path_ + self.c_Output_file_name + "_filtered.txt"
filtered_files_F = open(filtered_file_F, "w+")
# headers
AllHeadersFromFilteredFile_F = ""
AllHeadersFromFilteredFile_F = ("qseqid" + '\t' + "sacc" + '\t' + "stitle" + '\t' +
"qseq" + '\t' + "sseq" + '\t' + "nident" + '\t' + "mismatch" + '\t' +
"pident" + '\t' + "length" + '\t' + "evalue" + '\t' +
"bitscore" + '\t' + "qstart" + '\t' + "qend" + '\t' + "sstart" + '\t' +
"send" + '\t' + "gapopen" + '\t' + "gaps" + '\t' +
"qlen" + '\t' + "slen" + '\t' + "PercentageOverlap" + '\n')
filtered_files_F .write(AllHeadersFromFilteredFile_F)
# Reading files
tempstring = "temp"
while tempstring:
tempstring = file_F.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split('\t')
columns = (rowlist[qseqid] + '\t' + rowlist[sacc] + '\t' + rowlist[stitle] + '\t' +
rowlist[qseq] + '\t' + rowlist[sseq] + '\t' + rowlist[nident] + '\t' + rowlist[mismatch] + '\t' +
rowlist[pident] + '\t' + rowlist[length] + '\t' + rowlist[evalue] + '\t' +
rowlist[bitscore] + '\t' + rowlist[qstart] + '\t' + rowlist[qend] + '\t' + rowlist[
sstart] + '\t' +
rowlist[send] + '\t' + rowlist[gapopen] + '\t' + rowlist[gaps] + '\t' +
rowlist[qlen] + '\t' + rowlist[slen] + '\t')
Querylength_F = int(rowlist[qlen])
Length_F = int(rowlist[length])
SubjectLength_F = int(rowlist[slen])
min_length_F = min(Querylength_F, SubjectLength_F)
PercentageOverlap_F = (Length_F / min_length_F)
rowlist.append(str(PercentageOverlap_F))
columns = (rowlist[qseqid] + '\t' + rowlist[sacc] + '\t' + rowlist[stitle] + '\t' +
rowlist[qseq] + '\t' + rowlist[sseq] + '\t' + rowlist[nident] + '\t' + rowlist[mismatch] + '\t' +
rowlist[pident] + '\t' + rowlist[length] + '\t' + rowlist[evalue] + '\t' +
rowlist[bitscore] + '\t' + rowlist[qstart] + '\t' + rowlist[qend] + '\t' + rowlist[
sstart] + '\t' +
rowlist[send] + '\t' + rowlist[gapopen] + '\t' + rowlist[gaps] + '\t' +
rowlist[qlen] + '\t' + rowlist[slen] + '\t' + rowlist[PercentageOverlapINT] + '\n')
# FILTERING STEP 1 <<<<< DEFAULT "Percentage overlap >80% or 0.8" >>>>> AND <<<<< DEFAULT "BitScore >50" >>>
# HANDLES
if float(rowlist[PercentageOverlapINT]) >= float(self.d_Percentage_overlap):
if float(rowlist[bitscore]) >= int(self.e_bitscore):
filtered_files_F.write(columns)
file_F.close()
filtered_files_F.close()
# TO BE CHECKED
filtered_files_2_F = open(filtered_file_F, 'r')
###################################################################################################################################
#####################################################PART 3
# FILTERING STEP 2
filter_part2_path_and_name_F = self.b_Output_Path_ + self.c_Output_file_name + "_sorted.txt"
filtered_files_part2_F = open(filter_part2_path_and_name_F, "w")
# headers
AllHeadersFromFilteredFile_F = ""
AllHeadersFromFilteredFile_F = ("qseqid" + '\t' + "sacc" + '\t' + "stitle" + '\t' +
"qseq" + '\t' + "sseq" + '\t' + "nident" + '\t' + "mismatch" + '\t' +
"pident" + '\t' + "length" + '\t' + "evalue" + '\t' +
"bitscore" + '\t' + "qstart" + '\t' + "qend" + '\t' + "sstart" + '\t' +
"send" + '\t' + "gapopen" + '\t' + "gaps" + '\t' +
"qlen" + '\t' + "slen" + '\t' + "PercentageOverlap" + '\n')
filtered_files_part2_F.write(AllHeadersFromFilteredFile_F)
# Reading files
lst_lst = []
counter = 0
tempstring = "temp"
while tempstring:
tempstring = filtered_files_2_F.readline()
if tempstring == "":
break
if counter != 0:
templine = tempstring.splitlines()
x = templine[0]
rowlist_2 = x.split('\t')
lst_lst.append(rowlist_2)
columns = (rowlist_2[qseqid] + '\t' + rowlist_2[sacc] + '\t' + rowlist_2[stitle] + '\t' +
rowlist_2[qseq] + '\t' + rowlist_2[sseq] + '\t' + rowlist_2[nident] + '\t' + rowlist_2[
mismatch] + '\t' +
rowlist_2[pident] + '\t' + rowlist_2[length] + '\t' + rowlist_2[evalue] + '\t' +
rowlist_2[bitscore] + '\t' + rowlist_2[qstart] + '\t' + rowlist_2[qend] + '\t' + rowlist_2[
sstart] + '\t' +
rowlist_2[send] + '\t' + rowlist_2[gapopen] + '\t' + rowlist_2[gaps] + '\t' +
rowlist_2[qlen] + '\t' + rowlist_2[slen] + '\t' + rowlist_2[PercentageOverlapINT] + '\n')
counter += 1
# READ THE NEW FILE AND ENTER THE LOOP
# SORTING
list.sort(lst_lst, key=lambda DataRow_0: float(DataRow_0[pident]), reverse=True)
list.sort(lst_lst, key=lambda DataRow_2: float(DataRow_2[PercentageOverlapINT]), reverse=True)
list.sort(lst_lst, key=lambda DataRow_1: float(DataRow_1[bitscore]), reverse=True)
list.sort(lst_lst, key=lambda DataRow_3: DataRow_3[qseqid])
Dictionary_lst_lst = {}
# Reading list_list
length = len(lst_lst)
for i in range(length):
temp_rowlist = lst_lst[i]
temp_rowlist_length = len(temp_rowlist)
if temp_rowlist_length != 20:
print("length of tem_row_list_is:")
print(temp_rowlist_length)
continue
row_string_for_output = ""
Variable_QSeqID = temp_rowlist[qseqid]
try:
for j in range(temp_rowlist_length - 1):
temp_string = temp_rowlist[j]
row_string_for_output += (temp_string + "\t")
row_string_for_output += temp_rowlist[temp_rowlist_length - 1]
row_string_for_output += "\n"
except IndexError:
print("Exception thrown")
print(row_string_for_output)
# Tuple
TheTuple_rowlist = (Variable_QSeqID, row_string_for_output)
if Variable_QSeqID in Dictionary_lst_lst:
print("key already in dictionary")
else:
Dictionary_lst_lst[Variable_QSeqID] = row_string_for_output
filtered_files_part2_F.write(row_string_for_output)
filtered_files_part2_F.close()
filtered_files_2_F.close()
class Win1(Script1, Script2, Script3, Script4, Script55):
def __init__(self, window):
# Initializations
self.wind = window
self.wind.title("omicR")
self.wind.wm_iconbitmap('Currito.ico')
self.wind.resizable(False, False)
# Creating A Frame Container
frame = LabelFrame(self.wind, text="Select what would you like to do:")
frame.grid(row=0, column=0, columnspan=3, padx=40, pady=40)
# Buttons
tk.Button(frame, text="Create FASTA files and input files for BLAST / filtering",
command=self.new_window2).grid(row=3, columnspan=2, padx=5, pady=5, sticky=W + E)
tk.Button(frame, text="Download Genomes",
command=self.new_window3).grid(row=4, columnspan=2, padx=5, pady=5, sticky=W + E)
tk.Button(frame, text="Create Genome Database",
command=self.new_window4).grid(row=5, columnspan=2, padx=5, pady=5, sticky=W + E)
tk.Button(frame, text="BLAST / filtering", command=self.new_window5
).grid(row=6, columnspan=2, padx=5, pady=5, sticky=W + E)
tk.Button(frame, text="Filtering", command=self.new_window55
).grid(row=7, columnspan=2, padx=5, pady=5, sticky=W + E)
# Instructions
tk.Button(frame, text="Instructions", command=self.new_window6).grid(row=8, columnspan=2, padx=5, pady=5,
sticky=W + E)
# Close Button
tk.Button(frame, text="Close", command=self.close_window).grid(row=10, column=1, columnspan=2, padx=5, pady=5,
sticky=E)
# FASTA FILES
def new_window2(self):
self.new_window = tk.Toplevel(self.wind)
self.app = Win2(self.new_window)
# Download Genomes
def new_window3(self):
self.new_window = tk.Toplevel(self.wind)
self.app = Win3(self.new_window)
# Create Genome Database
def new_window4(self):
self.new_window = tk.Toplevel(self.wind)
self.app = Win4(self.new_window)
# BLAST and Filtering
def new_window5(self):
self.new_window = tk.Toplevel(self.wind)
self.app = Win5(self.new_window)
def new_window55(self):
self.new_window = tk.Toplevel(self.wind)
self.app = Win55(self.new_window)
# HELP
def new_window6(self):
self.new_window = tk.Toplevel(self.wind)
self.app = Win6(self.new_window)
def close_window(self):
self.wind.destroy()
# FASTA FILES
class Win2(Win1):
def __init__(self, window):
# Initializations
self.window = window
self.wind = window
self.wind.title("Create FASTA files and input files for BLAST filtering")
self.wind.wm_iconbitmap('Currito.ico')
# Creating a Frame Container
frame = LabelFrame(self.wind, text="Complete the following parameters ")
frame.grid(row=0, column=0, columnspan=3, padx=20, pady=20)
# CSV Input
# ROW1
# INPUT FILE PATH
Label(frame, text="Input file path (CSV file required): ").grid(row=1, column=0, sticky=W)
Label(frame, text="Example: " + "C:" + doubleBackSlash +
doubleBackSlash + "Users/MyDocuments/Bassiana.csv ").grid(row=1, column=6, sticky=W)
self.CSVInput = tk.Entry(frame)
self.CSVInput.focus()
self.CSVInput.grid(row=1, column=1, columnspan=2, ipadx=200, padx=5, pady=5, )
# Button Select
tk.Button(frame, text="Select", command=self.select_directory_CSV_input_path).grid(row=1, column=5,
sticky=W + E, padx=2, pady=2)
# Output File Path
# ROW 2
Label(frame, text="Output file path: ").grid(row=2, column=0, sticky=W)
Label(frame, text="Example: " + "C:" + doubleBackSlash +
doubleBackSlash + "Users/MyDocuments/ ").grid(row=2, column=6, sticky=W)
self.OutputFilePath = tk.Entry(frame)
self.OutputFilePath.grid(row=2, column=1, columnspan=2, ipadx=200, padx=5, pady=5, )
# Button Select
tk.Button(frame, text="Select", command=self.select_directory_output_path).grid(row=2, column=5, padx=2, pady=2)
# OUTPUT FILE NAME
# ROW 3
Label(frame, text="Output file name: ").grid(row=3, column=0, sticky=W)
Label(frame, text="Example: Bassiana_BLAST_Results ").grid(row=3, column=6, sticky=W)
self.CSVOutputFileName = tk.Entry(frame)
self.CSVOutputFileName.grid(row=3, column=1, columnspan=2, ipadx=200, padx=5, pady=5, )
# Row where header starts
# Row 4
Label(frame, text="Row where header starts: ").grid(row=4, column=0, sticky=W)
Label(frame, text="Example: 1 (Start counting rows from one *Number*").grid(row=4, column=2, sticky=W)
self.RowWhereHeaderStarts = tk.Entry(frame)
self.RowWhereHeaderStarts.grid(row=4, column=1, columnspan=1, ipadx=50, padx=5, pady=5, sticky=W)
# Row where data starts
# Row 5
Label(frame, text="Row where data starts: ").grid(row=5, column=0, sticky=W)
Label(frame, text="Example: 2 (Start counting rows from one *Number*)").grid(row=5, column=2, sticky=W)
self.RowWhereDataStarts = tk.Entry(frame)
self.RowWhereDataStarts.grid(row=5, column=1, columnspan=1, ipadx=50, padx=5, pady=5, sticky=W)
# Column of sequences
# Row 6
Label(frame, text="Column of Sequences: ").grid(row=6, column=0, sticky=W)
Label(frame, text="Example: 0 (Start counting columns from zero *Index*)").grid(row=6, column=2, sticky=W)
self.ColumnOfSequences = tk.Entry(frame)
self.ColumnOfSequences.grid(row=6, column=1, columnspan=1, ipadx=50, padx=5, pady=5, sticky=W)
# Column of AVGreads
# Row 7
#Label(frame, text="Column of comments [Average Reads]: ").grid(row=7, column=0, sticky=W)
#Label(frame, text="Example: 1 (Start counting columns from zero *Index*)").grid(row=7, column=2, sticky=W)
#self.ColumnOfAVGreads = tk.Entry(frame)
#self.ColumnOfAVGreads.grid(row=7, column=1, columnspan=1, ipadx=50, padx=5, pady=5, sticky=W)
# Column of N Bases
# Row 8
#Label(frame, text="Column of comments [NBases]: ").grid(row=8, column=0, sticky=W)
#Label(frame, text="Example: 2 (Start counting columns from zero *Index*)").grid(row=8, column=2, sticky=W)
#Label(frame, text=" ").grid(row=9, column=6, sticky=W)
#self.ColumnOfNbases = tk.Entry(frame)
#self.ColumnOfNbases.grid(row=8, column=1, columnspan=1, ipadx=50, padx=5, pady=5, sticky=W)
# WINDOW FASTA FILES
# Button clear
tk.Button(frame, text="Clear all", command=lambda: [self.ClearAll_Fasta_files()]).grid(row=17, column=6,
columnspan=1, padx=5,
pady=5,
sticky=W + E)
# Button Run
tk.Button(frame, text="Run", command=lambda: [self.Run_Button_FASTA_FILES()]).grid(row=18, column=6,
columnspan=1, padx=5, pady=5,
sticky=W + E)
# BUTTON Close
tk.Button(frame, text="Close", command=self.close_window).grid(row=19, column=6, columnspan=1, padx=5, pady=5,
sticky=W + E)
def Run_Button_FASTA_FILES(self):
TextFromCSVInput = self.CSVInput.get()
TextFromOutputPath = self.OutputFilePath.get()
TextFromOutputFileName = self.CSVOutputFileName.get()
TextFromRowWhereHeaderStarts = self.RowWhereHeaderStarts.get()
TextFromRowWhereDataStarts = self.RowWhereDataStarts.get()
TextFromSequenceColumn = self.ColumnOfSequences.get()
#TextFromAVG_reads = self.ColumnOfAVGreads.get()
#TextFrom_Nbases = self.ColumnOfNbases.get()
if (len(TextFromCSVInput) != 0
and len(TextFromOutputPath) != 0
and len(TextFromRowWhereHeaderStarts) != 0
and len(TextFromRowWhereDataStarts) != 0
and len(TextFromSequenceColumn)):
Script1.a_InputCSVFileName = TextFromCSVInput
TextFromOutputMod = TextFromOutputPath + doubleBackSlash
Script1.b_OutputPATH = TextFromOutputMod
if len(TextFromOutputFileName) != 0:
Script1.c_OutputFileName = TextFromOutputFileName
Script1.c_OutputFileName = TextFromOutputFileName
Script1.d_Row_Where_header_starts = int(TextFromRowWhereHeaderStarts)
Script1.e_rowWhereDataStarts = int(TextFromRowWhereDataStarts)
Script1.f_SEQUENCE_COLUMN = int(TextFromSequenceColumn)
#Script1.g_AVG_READS = int(TextFromAVG_reads)
#Script1.i_Nbases = int(TextFrom_Nbases)
print(Script1.a_InputCSVFileName)
print(Script1.b_OutputPATH)
print(Script1.c_OutputFileName)
print(Script1.d_Row_Where_header_starts)
print(Script1.e_rowWhereDataStarts)
print(Script1.f_SEQUENCE_COLUMN)
#print(Script1.g_AVG_READS)
#print(Script1.i_Nbases)
# Output Messages
self.message = Label(text="Running", fg='red').grid(row=19, column=2, columnspan=2, sticky=W + E, padx=5,
pady=5)
Script1.main(self)
self.message1 = Label(text="Completed!", fg='red').grid(row=19, column=2, columnspan=2, sticky=W + E,
padx=5,
pady=5)
messagebox.showinfo('Information', "Completed!")
else:
messagebox.showerror("Error", "All required parameters must be filled")
self.wind.lift()