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import gradio as gr |
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base_pairing = {'A':'U', 'U':'A', 'C':'G','G':'C'} |
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def transcribe(seq): |
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RNA_seq = seq.replace('T', 'U') |
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start_codon = RNA_seq.find('AUG') |
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codons = [] |
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for i in range(start_codon, len(RNA_seq), 3): |
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codon = RNA_seq[i:i + 3] |
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if len(codon)==3: |
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codons.append(codon) |
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return codons |
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translate = { |
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'UUU':'Phe','UCU':'Ser','UAU':'Tyr','UGU':'Cys', |
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'UUC':'Phe','UCC':'Ser','UAC':'Tyr','UGC':'Cys', |
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'UUA':'Leu','UCA':'Ser','UAA':'Stop','UGA':'Stop', |
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'UUG':'Leu','UCG':'Ser','UAG':'Stop','UGG':'Trp', |
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'CUU':'Leu','CCU':'Pro','CAU':'His','CGU':'Arg', |
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'CUC':'Leu','CCC':'Pro','CAC':'His','CGC':'Arg', |
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'CUA':'Leu','CCA':'Pro','CAA':'Gln','CGA':'Arg', |
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'CUG':'Leu','CCG':'Pro','CAG':'Gln','CGG':'Arg', |
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'AUU':'Ile','ACU':'Thr','AAU':'Asn','AGU':'Ser', |
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'AUC':'Ile','ACC':'Thr','AAC':'Asn','AGC':'Ser', |
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'AUA':'Ile','ACA':'Thr','AAA':'Lys','AGA':'Arg', |
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'AUG':'Met','ACG':'Thr','AAG':'Lys','AGG':'Arg', |
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'GUU':'Val','GCU':'Ala','GAU':'Asp','GGU':'Gly', |
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'GUC':'Val','GCC':'Ala','GAC':'Asp','GGC':'Gly', |
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'GUA':'Val','GCA':'Ala','GAA':'Glu','GGA':'Gly', |
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'GUG':'Val','GCG':'Ala','GAG':'Glu','GGG':'Gly' |
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} |
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AA_mapping = { |
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'Ala':'A', 'Arg':'R','Asn':'N', |
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'Asp':'D', 'Cys':'C','Gln':'Q', |
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'Glu':'E', 'Gly':'G','His':'H', |
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'Ile':'I', 'Leu':'L','Lys':'K', |
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'Met':'M', 'Phe':'F','Pro':'P', |
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'Ser':'S', 'Thr':'T','Trp':'W', |
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'Tyr':'Y','Val':'V' |
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} |
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def transcribe(seq): |
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RNA_seq = seq.replace('T', 'U') |
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reading_frames = [] |
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for pos in range(0,3): |
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codons = [] |
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for i in range(pos, len(RNA_seq), 3): |
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codon = RNA_seq[i:i + 3] |
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if len(codon)==3: |
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codons.append(codon) |
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reading_frames.append(codons) |
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RNA_seq_rev = RNA_seq[::-1] |
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cDNA = '' |
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for i in range(0, len(RNA_seq_rev)): |
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cDNA += base_pairing[RNA_seq_rev[i]] |
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for pos in range(0,3): |
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codons = [] |
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for i in range(pos, len(cDNA), 3): |
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codon = cDNA[i:i + 3] |
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if len(codon)==3: |
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codons.append(codon) |
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reading_frames.append(codons) |
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return reading_frames |
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def get_protein_from_DNA(DNA): |
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reading_frames =transcribe(DNA) |
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orf_list = [] |
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for i in range(len(reading_frames)): |
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mRNA = reading_frames[i] |
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one_letter='' |
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found_start = False |
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for codon in mRNA: |
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if codon =='AUG' and not found_start: |
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one_letter += '<' |
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found_start = True |
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if codon =='UAA' or codon=='UGA'or codon =='UAG': |
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if found_start: |
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one_letter += '>' |
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found_start = False |
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continue |
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one_letter += AA_mapping[translate[codon]] |
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if one_letter.find('M') != -1: |
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one_letter = '*' + one_letter + '>' |
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orf_list.append(one_letter) |
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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] |
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return r |
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input_module = gr.inputs.Textbox(label = "Enter your DNA sequence in the box:") |
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output_module = gr.outputs.Textbox(label = 'Protein sequences from ORFs 1-6:') |
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interface = gr.Interface(fn=get_protein_from_DNA, |
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inputs=input_module, |
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outputs=output_module, |
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title="CSCI1020 Demo 2: Web Application for DNA Transcription & RNA Translation", |
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description= "Click examples below for a quick demo", |
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theme = 'huggingface', |
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layout = 'vertical' |
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) |
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interface.launch() |
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