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TestingPyCharm_BLAST_filtering_and_all.py
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TestingPyCharm_BLAST_filtering_and_all.py
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#C:\Users\s433088\AppData\Local\Programs\Python\Python36-32\python.exe TestingPyCharm_BLAST_filtering_and_all.py
#-x C:\\thingslap\ncbi-blast-2.6.0+-x64-win64.tar\ncbi-blast-2.6.0+-x64-win64\ncbi-blast-2.6.0+\bin\
#-y dc-megablast
#-a C:\\thingslap\Pipeline\Output_files\Genomes\Chicken_vGRCg6a\Chicken_vGRCg6a.fasta
#-b C:\\thingslap\Pipeline\Output_files\Bassiana_364_M-365_F-64_F_contigs_ge_100.fasta
#-c C:\\thingslap\Pipeline\GUI_Output\Upload\
#-d Test2_Bassiana_Vs_chicken_PYTHON_2
#-e 11 -f 70 -g 4 -i 6 -j 0.01 -k 30
#-l C:\\thingslap\Pipeline\Output_files\Bassiana_364_M-365_F-64_F_contigs_ge_100_InputFile_with_unique_ID.txt
#C:\Users\s433088\AppData\Local\Programs\Python\Python36-32\python.exe TestingPyCharm_BLAST_filtering_and_all.py -x C:\\thingslap\ncbi-blast-2.6.0+-x64-win64.tar\ncbi-blast-2.6.0+-x64-win64\ncbi-blast-2.6.0+\bin\ -y FALSE -a C:\\thingslap\Pipeline\Output_files\Genomes\Chicken_vGRCg6a\Chicken_vGRCg6a.fasta -b C:\thingslap\Pipeline\GUI_Output\Upload\Bassiana_364_M-365_F-64_F_contigs_ge_100_for_testing.fasta -c C:\\thingslap\Pipeline\GUI_Output\Upload\ -d Test3_Bassiana_Vs_chicken_FALSE -e 11 -f 70 -g 4 -i 6 -j 0.01 -k 30 -l C:\\thingslap\Pipeline\GUI_Output\Upload\Bassiana_364_M-365_F-64_F_contigs_ge_100_for_testing_InputFile_with_unique_ID.txt
#C:\Users\s433088\AppData\Local\Programs\Python\Python36-32\python.exe BLAST_filtering_and_all.py
#-a C:\\thingslap\Pipeline\Output_files\Genomes\Chicken_vGRCg6a\Chicken_vGRCg6a.fasta
#-b C:\\thingslap\Pipeline\Output_files\Bassiana_364_M-365_F-64_F_contigs_ge_100.fasta
#-c C:\\thingslap\Pipeline\GUI_Output\Upload\
#-d Test_Bassiana_Vs_chicken_PYTHON
#-e 11 -f 70 -g 4 -i 6 -j 0.01 -k 30
#-l C:\\thingslap\Pipeline\Output_files\Bassiana_364_M-365_F-64_F_contigs_ge_100_InputFile_with_unique_ID.txt
import sys, getopt
import os
def main(argv):
x_Path_to_NCBI_Directory_BF = ""
y_DC_MegaBlast_BF = ""
a_Data_Base_fasta = ""
print(" the value of a_Data_Base_fasta is: " + a_Data_Base_fasta)
b_Query_fasta_file = ""
c_Output_Path_= ""
#BLAST PARAMETRES
d_Output_file_name = "_BLAST"
e_word_size = "" #"20"
f_Percentage_identity = ""#"70"
g_number_of_threads = "" # "4"
i_OutputFormat = "" # "6"
#FIlTERING PARAMETRES
j_Percentage_overlap = 0.8
k_bitscore = 50
l_InputFile_with_unique_ID = ""
try:
opts, args = getopt.getopt(argv,"x:y:a:b:c:d:e:f:g:i:j:k:l:",["x_Path_to_NCBI_Directory_BF=",
"y_DC_MegaBlast_BF=",
"a_Data_Base_fasta=",
"b_Query_fasta_file=",
"c_Output_Path_=",
"d_Output_file_name=",
"e_word_size=",
"f_Percentage_identity=",
"g_number_of_threads=",
"i_OutputFormat=",
"j_Percentage_overlap=",
"k_bitscore=",
"l_InputFile_with_unique_ID="])
except getopt.GetoptError:
print ("ERROR:")
print ('CHECK YOUR INPUT HANDLES')
print('BLAST_filtering_and_all.py -a <a_Data_Base_fasta> -b <b_Query_fasta_file> -c <c_Output_Path_> -d <d_Output_file_name> -e <e_word_size> -f <f_Percentage_identity> -g <g_number_of_threads> -i <i_OutputFormat> -j <j_Percentage_Overlap> -k <k_bitscore> -l <l_InputFile_with_unique_ID>')
sys.exit(2)
for opt, arg in opts:
if opt in ( '-h'):
print ("HELP")
print ('BLAST_filtering_and_all.py -a <a_Data_Base_fasta> -b <b_Query_fasta_file> -c <c_Output_Path_> -d <d_Output_file_name> -e <e_word_size> -f <f_Percentage_identity> -g <g_number_of_threads> -i <i_OutputFormat> -j <j_Percentage_Overlap> -k <k_bitscore> -l <l_InputFile_with_unique_ID>')
sys.exit()
elif opt in ("-x", "--x_Path_to_NCBI_Directory_BF"):
x_Path_to_NCBI_Directory_BF = arg
elif opt in ("-y", "--y_DC_MegaBlast_BF"):
#y_DC_MegaBlast_BF = ("-task " + arg)
if arg == "TRUE":
y_DC_MegaBlast_BF = "-task dc-megablast"
elif opt in ("-a", "--a_Data_Base_fasta"):
a_Data_Base_fasta = arg
elif opt in ("-b", "--b_Query_fasta_file"):
b_Query_fasta_file = arg
elif opt in ("-c", "--c_Output_Path_"):
c_Output_Path_ = arg
elif opt in ("-d", "--d_Output_file_name"):
d_Output_file_name = arg
elif opt in ("-e", "--e_word_size"):
e_word_size = arg
elif opt in ("-f", "--f_Percentage_identity"):
f_Percentage_identity = arg
elif opt in ("-g", "--g_number_of_threads"):
g_number_of_threads = arg
elif opt in ("-i", "--i_OutputFormat"):
i_OutputFormat = arg
elif opt in ("-j", "--j_Percentage_overlap"):
j_Percentage_overlap = float(arg)
elif opt in ("-k", "--k_bitscore"):
k_bitscore = int(arg)
elif opt in ("-l", "--l_InputFile_with_unique_ID"):
l_InputFile_with_unique_ID = arg
print('\n')
print("Percentage Overlap")
print(j_Percentage_overlap)
print('\n')
print("Bitscore")
print(k_bitscore)
print('\n')
CommandLine_BF = (x_Path_to_NCBI_Directory_BF + "blastn " + y_DC_MegaBlast_BF
+ " -db " + a_Data_Base_fasta + " -query "
+ b_Query_fasta_file + " -out " + c_Output_Path_ + d_Output_file_name + "BLAST.txt"
+ " -word_size " + e_word_size + " -perc_identity " + f_Percentage_identity
+ " -num_threads " + g_number_of_threads + " -outfmt " + '"' + 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 = c_Output_Path_ + d_Output_file_name + "BLAST.txt"
file_BF = open(BLAST_OUTPUT_FILE_BF, 'r')
filtered_file_BF = c_Output_Path_ + 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(j_Percentage_overlap):
if float(rowlist[bitscore]) >= int(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 = c_Output_Path_ + 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 = l_InputFile_with_unique_ID
Output_file_only_sequences_with_hits_BF = c_Output_Path_ + d_Output_file_name + "_only_sequences_with_hits.txt"
Output_final_BLAST_File_BF = c_Output_Path_ + 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()
if __name__ == "__main__":
main(sys.argv[1:])