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c034968 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 | import gradio as gr
import plotly.graph_objects as go
import plotly.express as px
from collections import Counter
import numpy as np
CODON_TABLE = {
'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', 'TAA': '*', 'TAG': '*',
'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', 'TGA': '*', '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',
}
COLOR_MAP = {'A': '#FF6B6B', 'T': '#4ECDC4', 'G': '#45B7D1', 'C': '#FFA07A'}
def analyze_dna(sequence):
seq = sequence.upper().replace(" ", "").replace("\n", "")
seq = ''.join(c for c in seq if c in 'ATGC')
if len(seq) < 3:
return "Enter at least 3 nucleotides", None, None, ""
# GC Content sliding window
window = min(50, len(seq) // 2) or 1
gc_values = []
for i in range(len(seq) - window + 1):
w = seq[i:i+window]
gc = (w.count('G') + w.count('C')) / len(w) * 100
gc_values.append(gc)
fig_gc = go.Figure()
fig_gc.add_trace(go.Scatter(
y=gc_values, mode='lines',
fill='tozeroy', fillcolor='rgba(78,205,196,0.2)',
line=dict(color='#4ECDC4', width=2)
))
fig_gc.update_layout(
title="GC Content (Sliding Window)",
xaxis_title="Position", yaxis_title="GC %",
template="plotly_dark", height=350,
paper_bgcolor='#0f1117', plot_bgcolor='#0f1117'
)
# Nucleotide composition
counts = Counter(seq)
fig_comp = px.pie(
names=list(counts.keys()),
values=list(counts.values()),
color=list(counts.keys()),
color_discrete_map=COLOR_MAP,
title="Nucleotide Composition"
)
fig_comp.update_layout(
template="plotly_dark", height=350,
paper_bgcolor='#0f1117', plot_bgcolor='#0f1117'
)
# Translate
protein = []
for i in range(0, len(seq) - 2, 3):
codon = seq[i:i+3]
aa = CODON_TABLE.get(codon, '?')
protein.append(aa)
protein_str = ''.join(protein)
stats = f"""### 📊 Sequence Statistics
- **Length:** {len(seq)} bp
- **GC Content:** {(seq.count('G')+seq.count('C'))/len(seq)*100:.1f}%
- **A:** {counts.get('A',0)} | **T:** {counts.get('T',0)} | **G:** {counts.get('G',0)} | **C:** {counts.get('C',0)}
- **Protein:** `{protein_str[:60]}{'...' if len(protein_str)>60 else ''}`"""
return stats, fig_gc, fig_comp, protein_str
demo = gr.Interface(
fn=analyze_dna,
inputs=gr.Textbox(label="DNA Sequence", lines=4,
placeholder="Paste DNA sequence (e.g., ATGCGATCGATCG...)"),
outputs=[
gr.Markdown(label="Statistics"),
gr.Plot(label="GC Content"),
gr.Plot(label="Composition"),
gr.Textbox(label="Protein Translation"),
],
title="🧬 DNA Sequence Visualizer",
description="Analyze and visualize DNA sequences with GC content, composition, and translation.",
theme=gr.themes.Soft(),
)
if __name__ == "__main__":
demo.launch() |