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Priyanka1207/crispreditease

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App README

EditEase

Flask conversion of the EditEase PHP project for Hugging Face Spaces.

Main modules

  • —Retrieve sequence from Ensembl Plants, NCBI, Gramene-style IDs, TAIR-style IDs, RGAP-style IDs, and configured Phytozome/JGI endpoints.
  • —Promoter motif analysis using PlantCARE/PlantPAN-style motif libraries.
  • —sgRNA design with PAM, GC%, ranking, off-target estimate, track visualization, and saved projects.
  • —Combined promoter + sgRNA workflow.
  • —Jobs, manual, team, visualization, and download pages.

Live data source behavior

The Retrieve page tries sources in this order:

  1. 1.Live source connector
  2. 2.data/local_sequences.json cache
  3. 3.demo sequence fallback, so the interface still shows a result

Supported live connectors:

  • —ensembl_plants: Ensembl REST gene/region/CDS sequence endpoints.
  • —ncbi: NCBI E-utilities ESearch/EFetch for Nuccore FASTA retrieval.
  • —gramene, tair, rgap: attempted through Ensembl Plants-compatible plant IDs first, then local fallback.
  • —phytozome: configure PHYTOZOME_SEQUENCE_URL and optionally JGI_API_TOKEN, because Phytozome/JGI access commonly requires an account/token or project-specific endpoint.

Optional environment variables:

bash
EDITEASE_ENABLE_REMOTE_FETCH=1
EDITEASE_REMOTE_TIMEOUT=12
NCBI_EMAIL=your_email@example.com
NCBI_API_KEY=your_ncbi_api_key
JGI_API_TOKEN=your_jgi_token
PHYTOZOME_SEQUENCE_URL=https://your-proxy-or-endpoint/{species}/{query}?region={region}&upstream={upstream}&downstream={downstream}

Run locally

bash
python -m venv .venv
.venv\Scripts\Activate.ps1   # Windows PowerShell
# source .venv/bin/activate   # Linux/Mac
pip install -r requirements.txt
python app.py

Open: http://127.0.0.1:7860

Upload to Hugging Face Spaces

Create a new Space with SDK = Docker, then upload all files from this folder. The app listens on port 7860.