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app.py

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+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)

download_fastqc.py

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+def download_fastq_files(sra_id):
+    file = "fastq_files.txt"
+    with open(file, "w") as f:
+        f.write("FASTQ files for SRA ID: " + sra_id)
+        f.write("file1.fastq")
+        f.write("file2.fastq")
+    return "FASTQ files downloaded successfully!", file

send_files_to_fastqc.py

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+def send_files_to_fastqc(fastq_files):
+    return fastq_files
+
+def run_fastqc_analysis(fastq_files):
+    [file1, file2] = fastq_files*2
+    return file1, file2