app.py

import gradio as gr

# Simulated functions for testing purposes
def download_fastq_files(sra_id):
    fastq_files = ["fastq_sample_1.fastq", "fastq_sample_2.fastq"]
    for file in fastq_files:
        print(f"Downloaded {file}")
    return f"Downloaded FASTQ files for {sra_id}", fastq_files

def send_files_to_fastqc(fastq_files):
    for file in fastq_files:
        print(f"Sent {file} to FASTQC")
    return f"Sent {fastq_files} to FASTQC"

def run_fastqc_analysis(fastq_files):
    file1, file2 = fastq_files
    return f"FASTQC analysis completed for {fastq_files}", file1, file2

def openURLinnewtab(url):
    url ['C:/Users/raanna/Desktop/NGS/2.html', 'C:/Users/raanna/Desktop/NGS/1.html']
    for file in url:
        print(f"Opening {file} in new tab")
        import webbrowser
        webbrowser.open_new_tab(url)


with gr.Blocks(title="NGS - Precision Medicine Toolkit") as app:
    gr.Markdown(value="# Step 1: Download FASTQ Files")
    with gr.Row():
        with gr.Column():
            sra_id = gr.Textbox(label="Enter SRA ID to download FASTQ Files", placeholder="e.g. SRR123456")
        with gr.Column():
            fastq_files = gr.Textbox(label="Downloaded FASTQ Files", interactive=False)
    download_fastq = gr.Button(value="Download FASTQ and Proceed to FASTQC")
    download_fastq.click(fn=download_fastq_files, inputs=[sra_id], outputs=[fastq_files])
    gr.Markdown(value="# Step 2: Perform FASTQC Analysis")
    with gr.Row():
        with gr.Column():
            fastq_analysis_files = gr.Textbox(label="FASTQ Files for Analysis", interactive=False)
        with gr.Column():
            fastqc_results = gr.Textbox(label="FASTQC Analysis Results", interactive=False)
    with gr.Row():
        run_fastqc = gr.Button(value="Run FASTQC and get Results")
        open_url = gr.Button(value="Open FASTQC Results in Browser")
    run_fastqc.click(fn=run_fastqc_analysis, inputs=[fastq_analysis_files], outputs=[fastqc_results])
    fastq_files.change(fn=lambda x: x, inputs=[fastq_files], outputs=[fastq_analysis_files])

    gr.Markdown(value="# Step 3: Perform FASTP Trimming and Analysis")

    
app.queue().launch(debug=True)