Skip to content

README.md

Latest commit

 

History

History
183 lines (149 loc) · 6.04 KB

README.md

File metadata and controls

183 lines (149 loc) · 6.04 KB

igv-streamlit

An unofficial Streamlit component for IGV (Integrative Genomics Viewer).

Supports both local files (served via a built-in CORS HTTP server) and remote URLs — no additional servers or configuration required.

Installation

pip install igv-streamlit

Or from source:

git clone https://github.com/yourname/igv-streamlit
pip install -e igv-streamlit/

Quick start

import igv_streamlit as sigv

# Built-in genome + remote BAM
sigv.igv_browser(
    genome="hg38",
    locus="BRCA1",
    tracks=[{
        "name": "Sample",
        "url":      "https://example.com/sample.bam",
        "indexURL": "https://example.com/sample.bam.bai",
        "type": "alignment",
    }],
)

Local files

Use path / indexPath / fastaPath instead of url / indexURL / fastaURL for local files.
The component automatically starts a CORS-enabled HTTP server and rewrites the paths to localhost URLs that igv.js can fetch.

import igv_streamlit as sigv

sigv.igv_browser(
    reference={
        "fastaPath": "/data/PlasmoDB-54_Pfalciparum3D7_Genome.fasta",
        "indexPath": "/data/PlasmoDB-54_Pfalciparum3D7_Genome.fasta.fai",
        "name": "Pf3D7",
    },
    locus="Pf3D7_01_v3:1-100000",
    tracks=[
        {
            "name": "Annotation",
            "path":   "/data/PlasmoDB-55_Pfalciparum3D7.gff",
            "format": "gff3",
            "type":   "annotation",
        },
        {
            "name":      "PF0833-C CRAM",
            "path":      "/data/PF0833-C.filtered.cram",
            "indexPath": "/data/PF0833-C.filtered.cram.crai",
            "format":    "cram",
            "type":      "alignment",
        },
        {
            "name":      "PF0833-C BAM",
            "path":      "/data/PF0833-C.filtered.bam",
            "indexPath": "/data/PF0833-C.filtered.bam.bai",
            "format":    "bam",
            "type":      "alignment",
        },
    ],
)

Path ↔ URL property mapping

Local file property igv.js URL property
path url
indexPath indexURL
fastaPath fastaURL
cytobandPath cytobandURL
aliasPath aliasURL

Remote files (PF8-release example)

import igv_streamlit as sigv

BASE = "https://pf8-release.cog.sanger.ac.uk"

sigv.igv_browser(
    reference={
        "fastaURL": f"{BASE}/reference/PlasmoDB-54-Pfalciparum3D7-Genome.fasta",
        "name": "PlasmoDB-54 Pf3D7",
    },
    locus="Pf3D7_01_v3:1-100000",
    tracks=[
        {
            "name": "Annotation",
            "url":    f"{BASE}/annotations/PlasmoDB-55_Pfalciparum3D7.gff.gz",
            "format": "gff3",
            "type":   "annotation",
        },
        {
            "name":     "PF0833-C",
            "url":      f"{BASE}/cram/PF0833-C.cram",
            "indexURL": f"{BASE}/cram/PF0833-C.cram.crai",
            "format":   "cram",
            "type":     "alignment",
        },
    ],
)

API reference

sigv.igv_browser(...)

Parameter Type Description
genome str | dict Built-in genome ID ("hg38", "mm10", …) or reference dict
reference dict Custom reference config with fastaURL/fastaPath
locus str Initial locus ("chr1:1000-2000" or gene name)
tracks list[dict] List of igv.js track config objects
height int Browser height in pixels (default: 500)
key str Streamlit component key for multiple browsers
on_locus_change callable Callback when the user navigates

Returns a Streamlit component result; access result.locus for the current locus string.

Running the demo app

git clone https://github.com/yourname/igv-streamlit
cd igv-streamlit
pip install -r requirements.txt

# optionally place genomic files in data/
mkdir -p data
# cp /path/to/*.bam data/ ...

streamlit run app.py

Architecture

┌─────────────────────────────────────────────────────┐
│  Streamlit app (Python)                             │
│                                                     │
│  igv_streamlit.igv_browser(reference=..., tracks=…) │
│    │                                                │
│    ├─ local path? → register_file(path)             │
│    │                  → http://127.0.0.1:PORT/file/TOKEN
│    │                                                │
│    └─ st.components.v2.component(data={config})     │
│         │                                           │
│         ▼                                           │
│  ┌─────────────────────────────────────┐           │
│  │  igv.js (loaded from CDN)           │           │
│  │  runs in main Streamlit page        │           │
│  │  fetches files via HTTP             │           │
│  │   remote → directly                │           │
│  │   local  → 127.0.0.1:PORT/file/…   │           │
│  └─────────────────────────────────────┘           │
│         │                                           │
│  locus changes → result.locus (Python)              │
└─────────────────────────────────────────────────────┘

Security note

The built-in file server only serves files that have been explicitly registered via path/indexPath/fastaPath properties. It does not expose arbitrary filesystem paths.

License

MIT