visuamitra 0.1.0__tar.gz

visuamitra-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: visuamitra
+Version: 0.1.0
+Summary: A Tandem Repeats visualization tool for Decomposition of Motifs and Methylation across alleles.
+License: MIT
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: fastapi
+Requires-Dist: uvicorn
+Requires-Dist: pysam
+Requires-Dist: pandas
+Requires-Dist: python-multipart
+Requires-Dist: bitarray
+Requires-Dist: regex
+
+# VisuaMiTRA
+Visualisation of Motif / Methylation in Tandem Repeat Alleles
+
+## Table of contents
+
+## Installation
+
+## Usage
+
+## Contacts

visuamitra-0.1.0/README.md

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+# VisuaMiTRA
+Visualisation of Motif / Methylation in Tandem Repeat Alleles
+
+## Table of contents
+
+## Installation
+
+## Usage
+
+## Contacts

visuamitra-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "visuamitra"
+version = "0.1.0"
+description = "A Tandem Repeats visualization tool for Decomposition of Motifs and Methylation across alleles."
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+dependencies = [
+    "fastapi",
+    "uvicorn",
+    "pysam",
+    "pandas",
+    "python-multipart",
+    "bitarray",
+    "regex"
+]
+
+[project.scripts]
+visuamitra = "visuamitra.main:run_server"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+# This ensures all your React build files are included in the pip wheel
+visuamitra = ["static/**/*"]

visuamitra-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

visuamitra-0.1.0/src/visuamitra/__init__.py

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+from .main import run_server
+
+__version__ = "0.1.0"

visuamitra-0.1.0/src/visuamitra/main.py

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+import os
+import time
+import logging
+import uvicorn
+from fastapi import FastAPI, Request
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.staticfiles import StaticFiles
+from fastapi.responses import FileResponse
+from .routes import router
+from pathlib import Path
+
+# Setup Logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger("timing")
+
+app = FastAPI(
+    title="Visuamitra Backend",
+    version="0.1.0"
+)
+
+# Timing Middleware
+@app.middleware("http")
+async def timing_middleware(request: Request, call_next):
+    start = time.perf_counter()
+    response = await call_next(request)
+    duration = time.perf_counter() - start
+    logger.info(f"{request.method} {request.url.path} took {duration:.3f}s")
+    return response
+
+# CORS Middleware (Keep this for local development)
+origins = ["http://localhost:3000", "http://127.0.0.1:3000", "http://192.168.14.145:3000"]
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+    expose_headers=["X-Next-Cursor"], 
+)
+
+# Include your API routes
+app.include_router(router, prefix="/api")
+
+# --- NEW: STATIC FILE SERVING LOGIC ---
+
+# 1. Determine where the static files are located
+# This assumes you copied the 'build' folder into 'backend/static'
+# In main.py
+from pathlib import Path
+
+# Use Pathlib for cleaner cross-platform path handling
+package_dir = Path(__file__).parent.resolve()
+static_dir = package_dir / "static"
+
+if static_dir.exists():
+    # Mount the /static/static subfolder
+    app.mount("/static", StaticFiles(directory=str(static_dir / "static")), name="static")
+    
+    @app.get("/{rest_of_path:path}")
+    async def serve_frontend(rest_of_path: str):
+        if rest_of_path.startswith("api/"):
+            return {"error": "API route not found"}
+        return FileResponse(str(static_dir / "index.html"))
+else:
+    # Fallback for development if static folder isn't built yet
+    @app.get("/")
+    def health_check():
+        return {"status": "Visuamitra backend running (Frontend build missing)"}
+
+# --- NEW: ENTRY POINT FOR PIP ---
+
+def run_server():
+    """Launcher for the visuamitra CLI command."""
+    import uvicorn
+    import webbrowser
+    from threading import Timer
+
+    port = 8088
+    url = f"http://127.0.0.1:{port}"
+
+    def open_browser():
+        webbrowser.open_new(url)
+
+    print(f"Starting VisuaMiTRa on {url}")
+    
+    # Optional: Automatically open the browser after 1.5 seconds
+    Timer(1.5, open_browser).start()
+
+    # We use the string import to avoid issues with signal handlers in some OS
+    uvicorn.run("visuamitra.main:app", host="127.0.0.1", port=port, reload=False)
+
+if __name__ == "__main__":
+    run_server()

visuamitra-0.1.0/src/visuamitra/routes.py

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+import os
+import shutil
+import tempfile
+from fastapi import APIRouter, UploadFile, File, Form, HTTPException
+from fastapi.responses import StreamingResponse
+import pysam
+from typing import Optional
+import base64
+
+from .visuamitra_script import visuamitra_data_extract_stream
+
+router = APIRouter()
+
+def encode_cursor(chr, pos):
+    raw = f"{chr}:{pos}"
+    return base64.urlsafe_b64encode(raw.encode()).decode()
+
+def decode_cursor(cursor):
+    try:
+        decoded = base64.urlsafe_b64decode(cursor.encode()).decode()
+        c, p = decoded.split(":")
+        return c, int(p)
+    except Exception:
+        raise HTTPException(status_code=400, detail="Invalid cursor format")
+
+@router.post("/vcf-to-tsv-cursor")
+async def vcf_to_tsv_cursor(
+    vcf: UploadFile = File(...),
+    tbi: UploadFile = File(...),
+    last_cursor: Optional[str] = Form(None),
+    page_size: int = Form(100),
+    chr: Optional[str] = Form(None),
+    start: Optional[int] = Form(None),
+    end: Optional[int] = Form(None),
+):
+    tmpdir = tempfile.mkdtemp(prefix="vcf_")
+    vcf_path = f"{tmpdir}/{vcf.filename}"
+    tbi_path = f"{tmpdir}/{tbi.filename}"
+
+    with open(vcf_path, "wb") as f:
+        shutil.copyfileobj(vcf.file, f)
+    with open(tbi_path, "wb") as f:
+        shutil.copyfileobj(tbi.file, f)
+
+    try:
+        tabix = pysam.TabixFile(vcf_path)
+    except Exception:
+        raise HTTPException(status_code=400, detail="Could not open VCF or index")
+
+    contigs = set(tabix.contigs)
+
+    # BASIC VALIDATION
+    if chr and chr not in contigs:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Chromosome '{chr}' not found in VCF"
+        )
+
+    if start is not None and start < 1:
+        raise HTTPException(status_code=400, detail="Start must be >= 1")
+    if end is not None and end < 1:
+        raise HTTPException(status_code=400, detail="End must be >= 1")
+    if start is not None and end is not None and start > end:
+        raise HTTPException(status_code=400, detail="Start must be <= End")
+
+    fetch_start = 0 if start is None else start - 1
+    fetch_end = end
+
+    # CRITICAL PREFLIGHT CHECK
+    try:
+        if chr:
+            # MUST run before streaming
+            has_any = False
+            for _ in tabix.fetch(chr, fetch_start, fetch_end):
+                has_any = True
+                break
+            if not has_any:
+                raise HTTPException(
+                    status_code=404,
+                    detail=f"No data found in range {start}-{end} on chromosome {chr}"
+                )
+
+        elif start is not None or end is not None:
+            found = False
+            for c in contigs:
+                try:
+                    for _ in tabix.fetch(c, fetch_start, fetch_end):
+                        found = True
+                        break
+                except ValueError:
+                    continue
+                if found:
+                    break
+
+            if not found:
+                raise HTTPException(
+                    status_code=404,
+                    detail=f"No data found in range {start}-{end} across all chromosomes"
+                )
+
+    except ValueError:
+        # pysam throws this for invalid regions
+        raise HTTPException(
+            status_code=400,
+            detail=f"Invalid genomic region: chr={chr}, start={start}, end={end}"
+        )
+
+    # CURSOR
+    cursor_chr, cursor_pos = (None, None)
+    if last_cursor:
+        cursor_chr, cursor_pos = decode_cursor(last_cursor)
+
+    collected = []
+    next_cursor = None
+    seen_header = False
+    count = 0
+
+    # SAFE STREAMING (no errors possible now)
+    for raw_line in visuamitra_data_extract_stream(vcf_path, chr, start, end):
+        if isinstance(raw_line, bytes):
+            raw_line = raw_line.decode("utf-8")
+
+        if not raw_line.strip():
+            continue
+
+        if raw_line.startswith("Chrom") and not seen_header:
+            collected.append(raw_line)
+            seen_header = True
+            continue
+
+        parts = raw_line.split("\t")
+        if len(parts) < 2:
+            continue
+
+        row_chr = parts[0]
+        try:
+            row_pos = int(parts[1])
+        except:
+            continue
+
+        if cursor_chr and row_pos <= cursor_pos and row_chr == cursor_chr:
+            continue
+
+        if count >= page_size:
+            next_cursor = encode_cursor(row_chr, row_pos)
+            break
+
+        collected.append(raw_line)
+        count += 1
+
+    def stream_rows():
+        for row in collected:
+            yield row
+
+    headers = {}
+    if next_cursor:
+        headers["X-Next-Cursor"] = next_cursor
+
+    return StreamingResponse(
+        stream_rows(),
+        media_type="text/tab-separated-values",
+        headers=headers,
+    )

visuamitra-0.1.0/src/visuamitra/static/asset-manifest.json

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+}

visuamitra-0.1.0/src/visuamitra/static/index.html

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+<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" type="image/png" href="/favicon.png?v=2"/><title>Visuamitra-Atharva</title><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Web site created using create-react-app"/><link rel="apple-touch-icon" href="/logo192.png"/><link rel="manifest" href="/manifest.json"/><title>React App</title><script defer="defer" src="/static/js/main.e7e8d878.js"></script><link href="/static/css/main.f5222080.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>

visuamitra-0.1.0/src/visuamitra/static/manifest.json

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+{
+  "short_name": "React App",
+  "name": "Create React App Sample",
+  "icons": [
+    {
+      "src": "favicon.ico",
+      "sizes": "64x64 32x32 24x24 16x16",
+      "type": "image/x-icon"
+    },
+    {
+      "src": "logo192.png",
+      "type": "image/png",
+      "sizes": "192x192"
+    },
+    {
+      "src": "logo512.png",
+      "type": "image/png",
+      "sizes": "512x512"
+    }
+  ],
+  "start_url": ".",
+  "display": "standalone",
+  "theme_color": "#000000",
+  "background_color": "#ffffff"
+}

visuamitra-0.1.0/src/visuamitra/static/robots.txt

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+# https://www.robotstxt.org/robotstxt.html
+User-agent: *
+Disallow:

visuamitra-0.1.0/src/visuamitra/static/static/css/main.f5222080.css

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