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import gradio as gr | |
DNA = 'GGTCAGAAAAAGCCCTCTCCATGTCTACTCACGATACATCCCTGAAAACCACTGAGGAAGTGGCTTTTCAGATCATCTTGCTTTGCCAGTTTGGGGTTGGGACTTTTGCCAATGTATTTCTCTTTGTCTATAATTTCTCTCCAATCTCGACTGGTTCTAAACAGAGGCCCAGACAAGTGATTTTAAGACACATGGCTGTGGCCAATGCCTTAACTCTCTTCCTCACTATATTTCCAAACAACATGATGACTTTTGCTCCAATTATTCCTCAAACTGACCTCAAATGTAAATTAGAATTCTTCACTCGCCTCGTGGCAAGAAGCACAAACTTGTGTTCAACTTGTGTTCTGAGTATCCATCAGTTTGTCACACTTGTTCCTGTTAATTCAGGTAAAGGAATACTCAGAGCAAGTGTCACAAACATGGCAAGTTATTCTTGTTACAGTTGTTGGTTCTTCAGTGTCTTAAATAACATCTACATTCCAATTAAGGTCACTGGTCCACAGTTAACAGACAATAACAATAACTCTAAAAGCAAGTTGTTCTGTTCCACTTCTGATTTCAGTGTAGGCATTGTCTTCTTGAGGTTTGCCCATGATGCCACATTCATGAGCATCATGGTCTGGACCAGTGTCTCCATGGTACTTCTCCTCCATAGACATTGTCAGAGAATGCAGTACATATTCACTCTCAATCAGGACCCCAGGGGCCAAGCAGAGACCACAGCAACCCATACTATCCTGATGCTGGTAGTCACATTTGTTGGCTTTTATCTTCTAAGTCTTATTTGTATCATCTTTTACACCTATTTTATATATTCTCATCATTCCCTGAGGCATTGCAATGACATTTTGGTTTCGGGTTTCCCTACAATTTCTCCTTTACTGTTGACCTTCAGAGACCCTAAGGGTCCTTGTTCTGTGTTCTTCAACTGTTGAAAGCCAGAGTCACTAAAAATGCCAAACACAGAAGACAGCTTTGCTAATACCATTAAATACTTTATTCCATAAATATGTTTTTAAAAGCTTGTATGAACAAGGTATGGTGCTCACTGCTATACTTATAAAAGAGTAAGGTTATAATCACTTGTTGATATGAAAAGATTTCTGGTTGGAATCTGATTGAAACAGTGAGTTATTCACCACCCTCCATTCTCT' | |
base_pairing = {'A':'U', 'U':'A', 'C':'G','G':'C'} | |
def transcribe(seq): | |
RNA_seq = seq.replace('T', 'U') | |
### Define location of start codon (AUG) | |
start_codon = RNA_seq.find('AUG') | |
codons = [] | |
for i in range(start_codon, len(RNA_seq), 3): | |
codon = RNA_seq[i:i + 3] | |
if len(codon)==3: | |
codons.append(codon) | |
return codons | |
####################################################################################### | |
# define dictionary to translate three-letter mRNA to three-letter amino acid here | |
####################################################################################### | |
translate = { | |
'UUU':'Phe','UCU':'Ser','UAU':'Tyr','UGU':'Cys', | |
'UUC':'Phe','UCC':'Ser','UAC':'Tyr','UGC':'Cys', | |
'UUA':'Leu','UCA':'Ser','UAA':'Stop','UGA':'Stop', | |
'UUG':'Leu','UCG':'Ser','UAG':'Stop','UGG':'Trp', | |
'CUU':'Leu','CCU':'Pro','CAU':'His','CGU':'Arg', | |
'CUC':'Leu','CCC':'Pro','CAC':'His','CGC':'Arg', | |
'CUA':'Leu','CCA':'Pro','CAA':'Gln','CGA':'Arg', | |
'CUG':'Leu','CCG':'Pro','CAG':'Gln','CGG':'Arg', | |
'AUU':'Ile','ACU':'Thr','AAU':'Asn','AGU':'Ser', | |
'AUC':'Ile','ACC':'Thr','AAC':'Asn','AGC':'Ser', | |
'AUA':'Ile','ACA':'Thr','AAA':'Lys','AGA':'Arg', | |
'AUG':'Met','ACG':'Thr','AAG':'Lys','AGG':'Arg', | |
'GUU':'Val','GCU':'Ala','GAU':'Asp','GGU':'Gly', | |
'GUC':'Val','GCC':'Ala','GAC':'Asp','GGC':'Gly', | |
'GUA':'Val','GCA':'Ala','GAA':'Glu','GGA':'Gly', | |
'GUG':'Val','GCG':'Ala','GAG':'Glu','GGG':'Gly' | |
} | |
####################################################################################### | |
# define dictionary to map three-letter amino acid to one-letter amino acid here | |
####################################################################################### | |
AA_mapping = { | |
'Ala':'A', 'Arg':'R','Asn':'N', | |
'Asp':'D', 'Cys':'C','Gln':'Q', | |
'Glu':'E', 'Gly':'G','His':'H', | |
'Ile':'I', 'Leu':'L','Lys':'K', | |
'Met':'M', 'Phe':'F','Pro':'P', | |
'Ser':'S', 'Thr':'T','Trp':'W', | |
'Tyr':'Y','Val':'V' | |
} | |
def transcribe(seq): | |
RNA_seq = seq.replace('T', 'U') | |
reading_frames = [] | |
# forward strand | |
for pos in range(0,3): | |
codons = [] | |
for i in range(pos, len(RNA_seq), 3): | |
codon = RNA_seq[i:i + 3] | |
if len(codon)==3: | |
codons.append(codon) | |
reading_frames.append(codons) | |
# # reverse strand | |
RNA_seq_rev = RNA_seq[::-1] | |
cDNA = '' | |
for i in range(0, len(RNA_seq_rev)): | |
cDNA += base_pairing[RNA_seq_rev[i]] | |
for pos in range(0,3): | |
codons = [] | |
for i in range(pos, len(cDNA), 3): | |
codon = cDNA[i:i + 3] | |
if len(codon)==3: | |
codons.append(codon) | |
reading_frames.append(codons) | |
return reading_frames | |
def find_complimentary_dna(dna_to_compliemnt): | |
_complement_seq = '' | |
for pos in range(0,len(dna_to_compliemnt)): | |
_last_char = dna_to_compliemnt[len(dna_to_compliemnt)-pos-1] | |
if _last_char == 'A': | |
_complement_seq = _complement_seq + 'A' | |
elif _last_char == 'T': | |
_complement_seq = _complement_seq + 'U' | |
elif _last_char == 'G': | |
_complement_seq = _complement_seq + 'G' | |
elif _last_char == 'C': | |
_complement_seq = _complement_seq + 'C' | |
return _complement_seq | |
def get_protein_from_DNA(DNA): | |
reading_frames =transcribe(DNA) | |
orf_list = [] | |
for i in range(len(reading_frames)): | |
mRNA = reading_frames[i] | |
one_letter='' | |
found_start = False | |
for codon in mRNA: | |
if codon =='AUG' and not found_start: | |
one_letter += '<' | |
found_start = True | |
if codon =='UAA' or codon=='UGA'or codon =='UAG': | |
if found_start: | |
one_letter += '>' | |
found_start = False | |
continue | |
one_letter += AA_mapping[translate[codon]] | |
# mark the valid orf found | |
if one_letter.find('M') != -1: | |
one_letter = '*' + one_letter + '>' | |
orf_list.append(one_letter) | |
r = " * means the ORF sequence exists and highlighted in as <>; \n5'to 3' Frame 1:"+ orf_list[0] +"\n5'to 3' Frame 2:" + orf_list[1] + "\n5'to 3' Frame 3:" + orf_list[2] + "\n3'to 5' Frame 1:" + orf_list[3] + "\n3'to 5' Frame 2:" + orf_list[4] + "\n3'to 5' Frame 3:"+orf_list[5] | |
return DNA, find_complimentary_dna(DNA), r | |
input1 = gr.inputs.Textbox(label = 'DNA sequence') | |
output1 = gr.outputs.Textbox(label = 'Primary Sequence') | |
output2 = gr.outputs.Textbox(label = 'Complimentary Sequence') | |
output3 = gr.outputs.Textbox(label = 'Open Reading Frames') | |
interface = gr.Interface(fn=get_protein_from_DNA, | |
inputs=input1, | |
outputs=[output1,output2,output3], | |
title="CSCI1020: Web Application for Transcription/Translation", | |
description= "A quick tool for translating a DNA sequence into a protein sequence", | |
theme = 'huggingface', | |
layout = 'vertical' | |
) | |
interface.launch() |