Proteins are chains of amino acids. Amino acids are coded by codons, a sequence of 3 DNA/RNA molecules. DNA also has 3 open reading frames. This is basically the DNA sequence, but shift it by 1 (i.e. ignore the first entry). Thus, you will have 3 different translations (no skipping, skip 1st entry, skip 2nd entry). Additionally, for some sequencing techniques, the length of the DNA they can sequence is short. Thus, you may need to sequence forward, and backwards (-f and -r in my code). Finally, these amino acids sequences start with a specific codon, and end with specific codons.
This code takes the DNA, translates it to an amino acid using the start and stop codons as borders. It offers the user 3 options, either only forward sequencing or reverse sequencing (where the dna sequence needs to be reversed, and then complemented), or a combination using both the forward and reverse. If both is picked, the script then looks for a point of intersection, and combines the forward and reverse at that intersection. Furthermore, it offers the user to pick between all the potential sequences found.
Finally, it uses BLAST to search the sequence picked against a database, to confirm the identity of the protein.
A basic schematic:
#DNA
AGTTGCGC
#translated
1st reading frame: MC
2nd reading frame: VA
3rd reading frame: LR
#since only 1st reading frame has seq that starts with M
#sequence to search
MC
#Blast will search MC
That's the basic idea.
To run: python script.py -f forward_file.txt -r reverse_file.txt
The correct option to pick when presented with the translations is 1 and 0
from selenium import webdriver
from selenium.webdriver.common.keys import Keys
import sys
dna_codon_dict={'TTT':'F','TTC':'F',
'TTA':'L','TTG':'L',
'CTT':'L','CTC':'L',
'CTA':'L','CTG':'L',
'ATT':'I','ATC':'I',
'ATA':'I','ATG':'M',
'GTT':'V','GTC':'V',
'GTA':'V','GTG':'V',
'TCT':'S','TCC':'S',
'TCA':'S','TCG':'S',
'CCT':'P','CCC':'P',
'CCA':'P','CCG':'P',
'ACT':'T','ACC':'T',
'ACA':'T','ACG':'T',
'GCT':'A','GCC':'A',
'GCA':'A','GCG':'A',
'TAT':'Y','TAC':'Y',
'CAT':'H','CAC':'H',
'CAA':'Q','CAG':'Q',
'AAT':'N','AAC':'N',
'AAA':'K','AAG':'K',
'GAT':'D','GAC':'D',
'GAA':'E','GAG':'E',
'TGT':'C','TGC':'C',
'TGG':'W','CGT':'R',
'CGC':'R','CGA':'R',
'CGG':'R','AGT':'S',
'AGC':'S','AGA':'R',
'AGG':'R','GGT':'G',
'GGC':'G','GGA':'G',
'GGG':'G'}
DNA_complement_dict={'A':'T',
'T':'A',
'G':'C',
'C':'G',
'N':'N'}
def load_file(files):
codon_list=[]
with open(files) as seq_result:
for lines in seq_result:
if lines.startswith('>') is True:
continue
remove_white_spaces=lines.strip().upper()
for codon in remove_white_spaces:
codon_list.append(codon)
return codon_list
def rev(files):
reverse_codon_list=[]
codon_list=load_file(files)
codon_list.reverse()
for codons in codon_list:
reversed_codon=DNA_complement_dict[codons]
reverse_codon_list.append(reversed_codon)
return reverse_codon_list
def codon_translation(global_codon_list):
codon_counter=0
codon_triple_list=[]
open_reading_frame_lists=[[],[],[],]
for i in range(3):
open_reading_frame_count=1
codon_triple_list.clear()
codon_counter=0
for codons in global_codon_list:
if open_reading_frame_count>=(i+1):
codon_counter+=1
codon_triple_list.append(codons)
if codon_counter == 3:
codon_counter=0
join_codons=''.join(codon_triple_list)
try:
amino_acid=dna_codon_dict[join_codons]
open_reading_frame_lists[i].append(amino_acid)
except:
pass
if join_codons in {'TAA','TAG','TGA'}:
open_reading_frame_lists[i].append('X')
codon_triple_list.clear()
else:
open_reading_frame_count+=1
return open_reading_frame_lists
def find_open_reading_frames(global_codon_list):
sequences_to_search=[]
sequence_to_add_to_search_list=[]
add_to_string=False
for open_reading_frames in codon_translation(global_codon_list):
for amino_acids in open_reading_frames:
if amino_acids == 'M':
add_to_string=True
if add_to_string is True:
sequence_to_add_to_search_list.append(amino_acids)
if amino_acids == 'X':
add_to_string=False
if len(sequence_to_add_to_search_list)>0:
sequences_to_search.append(''.join(sequence_to_add_to_search_list))
sequence_to_add_to_search_list.clear()
else:
sequence_to_add_to_search_list.clear()
return sequences_to_search
def forward_loop():
files=sys.argv[2]
forward_flag=False
if sys.argv[1] == '-f':
forward_flag=True
if forward_flag is True:
codon_list=load_file(files)
return codon_list
def reverse_loop():
if sys.argv[1] == '-f':
revsere_flag=False
try:
if sys.argv[3] == '-r':
files=sys.argv[4]
reverse_flag=True
if reverse_flag is True:
codon_list=rev(files)
return codon_list
except:
pass
else:
files=sys.argv[2]
reverse_flag=False
if sys.argv[1] == '-r':
reverse_flag=True
if reverse_flag is True:
codon_list=rev(files)
return codon_list
def overlay(sequence_list1,sequence_list2):
new_list1=[word for line in sequence_list1 for word in line]
new_list2=[word for line in sequence_list2 for word in line]
temp_list=[]
modified_list1=[]
counter=0
for x in new_list1:
temp_list.append(x)
modified_list1.append(x)
counter+=1
if counter >= 5:
if temp_list == new_list2[0:5]:
break
else:
temp_list.pop((0))
del new_list2[0:5]
return ''.join(modified_list1+new_list2)
sequence_list1=[]
sequence_list2=[]
global_codon_list=[]
def main_loop():
global global_codon_list
global sequence_list1
global sequence_list2
if sys.argv[1] == '-f':
global_codon_list=forward_loop()
sequences_to_search=find_open_reading_frames(global_codon_list)
sequence_to_search=[]
for sequence,number in zip(sequences_to_search,range(len(sequences_to_search))):
print(f'row {number} sequence: {sequence}')
sequence_to_search.append(sequence)
pick_sequence_to_search=input('indicate which row # sequence to search: ')
sequence_list1.append(sequence_to_search[int(pick_sequence_to_search)])
try:
if sys.argv[3] == '-r':
global_codon_list=reverse_loop()
sequences_to_search=find_open_reading_frames(global_codon_list)
sequence_to_search=[]
for sequence,number in zip(sequences_to_search,range(len(sequences_to_search))):
print(f'row {number} sequence: {sequence}')
sequence_to_search.append(sequence)
pick_sequence_to_search=input('indicate which row # sequence to search: ')
sequence_list2.append(sequence_to_search[int(pick_sequence_to_search)])
except:
pass
else:
sequence_to_search=[]
global_codon_list=reverse_loop()
sequences_to_search=find_open_reading_frames(global_codon_list)
for sequence,number in zip(sequences_to_search,range(len(sequences_to_search))):
print(f'row {number} sequence: {sequence}')
sequence_to_search.append(sequence)
pick_sequence_to_search=input('indicate which row # sequence to search: ')
sequence_list1.append(sequence_to_search[int(pick_sequence_to_search)])
main_loop()
driver = webdriver.Chrome()
driver.get('https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome')
fill_box = driver.find_element_by_xpath('/html/body/div[2]/div/div[2]/form/div[3]/fieldset/div[1]/div[1]/textarea')
fill_box.clear()
fill_box.send_keys(overlay(sequence_list1,sequence_list2))
sumbit_button=driver.find_element_by_xpath('/html/body/div[2]/div/div[2]/form/div[6]/div/div[1]/div[1]/input')
sumbit_button.click()
#DNA forward
>Delta_fl_pETDuet_1F
NNNNNNNNNNNNNNNNANTTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTT
GTTTAACTTTAAGAAGGAGATATACCATGGGCAGCAGCCATCACCATCATCACCACAGCCAGGATCCAATGATTCGGTTG
TACCCGGAACAACTCCGCGCGCAGCTCAATGAAGGGCTGCGCGCGGCGTATCTTTTACTTGGTAACGATCCTCTGTTATT
GCAGGAAAGCCAGGACGCTGTTCGTCAGGTAGCTGCGGCACAAGGATTCGAAGAACACCACACTTTTTCCATTGATCCCA
ACACTGACTGGAATGCGATCTTTTCGTTATGCCAGGCTATGAGTCTGTTTGCCAGTCGACAAACGCTATTGCTGTTGTTA
CCAGAAAACGGACCGAATGCGGCGATCAATGAGCAACTTCTCACACTCACCGGACTTCTGCATGACGACCTGCTGTTGAT
CGTCCGCGGTAATAAATTAAGCAAAGCGCAAGAAAATGCCGCCTGGTTTACTGCGCTTGCGAATCGCAGCGTGCAGGTGA
CCTGTCAGACACCGGAGCAGGCTCAGCTTCCCCGCTGGGTTGCTGCGCGCGCAAAACAGCTCAACTTAGAACTGGATGAC
GCGGCAAATCAGGTGCTCTGCTACTGTTATGAAGGTAACCTGCTGGCGCTGGCTCAGGCACTGGAGCGTTTATCGCTGCT
CTGGCCAGACGGCAAATTGACATTACCGCGCGTTGAACAGGCGGTGAATGATGCCGCGCATTTCACCCCTTTTCATTGGG
TTGATGCTTTGTTGATGGGAAAAAGTAAGCGCGCATTGCATATTCTTCAGCAACTGCGTCTGGAAGGCAGCGAACCGGTT
ATTTTGTTGCGCACATTAN
#DNA Reverse
>Delta_FL_pETDuet_R-T7-Term_B12.ab1
NNNNNNNNNNNNNAGCTGCGCTAGTAGACGAGTCCATGTGCTGGCGTTCAAATTTCGCAGCAGCGGTTTCTTTACCAGAC
TCGAGTTAACCGTCGATAAATACGTCCGCCAGGGGTTTATGGCACAACAGAAGAGATAACCCTTCCAGCTCTGCCCACAC
TGACTGACCGTAATCTTGTTTGAGGGTGAGTTCCGTTCGTGTCAGGAGTTGCACGGCCTGACGTAACTGCGTCTGACTTA
AGCGATTTAACGCCTCGCCCATCATGCCCCGGCGGTTCTGCCATACCCGATGCTTATCAAACAACGCACGCAGTGGCGTA
TGGGCAGACTGGCGTTTCAGGTTAACCAGTAACAACAGTTCACGTTGTAATGTGCGCAACAAAATAACCGGTTCGCTGCC
TTCCAGACGCAGTTGCTGAAGAATATGCAATGCGCGCTTACTTTTTCCCATCAACAAAGCATCAACCCAATGAAAAGGGG
TGAAATGCGCGGCATCATTCACCGCCTGTTCAACGCGCGGTAATGTCAATTTGCCGTCTGGCCAGAGCAGCGATAAACGC
TCCAGTGCCTGAGCCAGCGCCAGCAGGTTACCTTCATAACAGTAGCAGAGCACCTGATTTGCCGCGTCATCCAGTTCTAA
GTTGAGCTGTTTTGCGCGCGCAGCAACCCAGCGGGGAAGCTGAGCCTGCTCCGGTGTCTGACAGGTCACCTGCACGCTGC
GATTCGCAAGCGCAGTAAACCACGCGGCATTTTCTTGCGCTTTGCTTAATTTATTACCGCGGACGATCAACAGCNNNCGT
CATGCAGAAGTCCGGTGAGTGTGAGAAGTTGCTCATNGATCGCCCGCATTCGGNCCGTTTTCTGGTANCANCAGNNATAC
CGTTTGTCGANTGGCAAACANACN
