app.py

from __future__ import print_function
import gradio as gr
import requests
from Bio import SeqIO

def calculate_gc_content(sequence):
    """Calculate the GC content of a given sequence."""
    if len(sequence) == 0:
        return 0.0
    gc_count = sum(1 for base in sequence if base in 'GCgc')
    return (gc_count / len(sequence)) * 100

def fetch_fasta_info(url, block_size):
    min_gc = float('inf')
    max_gc = float('-inf')

    # Check if the URL is accessible
    try:
        response = requests.head(url)
        response.raise_for_status()  # Raise an error for bad responses
    except requests.RequestException:
        return None, None, "The URL is not accessible."

    # Download the FASTA file
    try:
        fasta_response = requests.get(url)
        fasta_response.raise_for_status()  # Raise an error for bad responses
    except requests.RequestException:
        return None, None, "Failed to download the FASTA file."

    # Save the content to a temporary file
    fasta_file = "temp.fasta"
    with open(fasta_file, 'wb') as f:
        f.write(fasta_response.content)

    # Parse the FASTA file and calculate GC content
    try:
        recs = SeqIO.parse(fasta_file, 'fasta')

        for rec in recs:
            if 'SO=chromosome' not in rec.description:
                continue
            
            size = len(rec.seq)
            num_blocks = size // block_size + 1

            for block in range(num_blocks):
                start = block_size * block
                end = size if block == num_blocks - 1 else block_size + start
                block_seq = rec.seq[start:end]
                block_gc = calculate_gc_content(block_seq)

                min_gc = min(min_gc, block_gc)
                max_gc = max(max_gc, block_gc)

    except Exception as e:
        return None, None, str(e)

    return min_gc, max_gc, None

# Create the Gradio interface
iface = gr.Interface(
    fn=fetch_fasta_info,
    inputs=[
        gr.Textbox(
            label="Enter FASTA URL",
            placeholder="Ex: https://example.com/path/to/your.fasta"
        ),
        gr.Slider(
            label="Block Size",
            minimum=1000,
            maximum=100000,
            step=1000,
            value=50000
        )
    ],
    outputs=[
        gr.Textbox(label="Min GC Content", placeholder="Min GC"),
        gr.Textbox(label="Max GC Content", placeholder="Max GC")
    ],
    title="GC Content Calculator",
    description="Enter a URL of a FASTA file to calculate GC content."
)

# Launch the app
iface.launch()