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import gradio as gr
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def download_fastq_files(sra_id):
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fastq_files = ["fastq_sample_1.fastq", "fastq_sample_2.fastq"]
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for file in fastq_files:
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print(f"Downloaded {file}")
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return f"Downloaded FASTQ files for {sra_id}", fastq_files
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def send_files_to_fastqc(fastq_files):
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for file in fastq_files:
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print(f"Sent {file} to FASTQC")
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return f"Sent {fastq_files} to FASTQC"
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def run_fastqc_analysis(fastq_files):
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file1, file2 = fastq_files
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return f"FASTQC analysis completed for {fastq_files}", file1, file2
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def openURLinnewtab(url):
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url ['C:/Users/raanna/Desktop/NGS/2.html', 'C:/Users/raanna/Desktop/NGS/1.html']
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for file in url:
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print(f"Opening {file} in new tab")
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import webbrowser
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webbrowser.open_new_tab(url)
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with gr.Blocks(title="NGS - Precision Medicine Toolkit") as app:
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gr.Markdown(value="# Step 1: Download FASTQ Files")
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with gr.Row():
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with gr.Column():
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sra_id = gr.Textbox(label="Enter SRA ID to download FASTQ Files", placeholder="e.g. SRR123456")
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with gr.Column():
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fastq_files = gr.Textbox(label="Downloaded FASTQ Files", interactive=False)
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download_fastq = gr.Button(value="Download FASTQ and Proceed to FASTQC")
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download_fastq.click(fn=download_fastq_files, inputs=[sra_id], outputs=[fastq_files])
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gr.Markdown(value="# Step 2: Perform FASTQC Analysis")
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with gr.Row():
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with gr.Column():
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fastq_analysis_files = gr.Textbox(label="FASTQ Files for Analysis", interactive=False)
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with gr.Column():
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fastqc_results = gr.Textbox(label="FASTQC Analysis Results", interactive=False)
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with gr.Row():
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run_fastqc = gr.Button(value="Run FASTQC and get Results")
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open_url = gr.Button(value="Open FASTQC Results in Browser")
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run_fastqc.click(fn=run_fastqc_analysis, inputs=[fastq_analysis_files], outputs=[fastqc_results])
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fastq_files.change(fn=lambda x: x, inputs=[fastq_files], outputs=[fastq_analysis_files])
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gr.Markdown(value="# Step 3: Perform FASTP Trimming and Analysis")
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app.queue().launch(debug=True) |
