blastweb 0.1.4

A simple web UI and API for running BLAST+ against local databases.

blastweb

Local BLAST search via Web UI and REST API using Flask.

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🐍 Requirements

• Python 3.8 over
• NCBI BLAST+（ include makeblastdb, blastdbcmd）
  • BLAST+ can be downloaded from here https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html

📦 Installation

Prepare venv: (Highly recommended)

python -m venv my_blastweb
source my_blastweb/bin/activate

from github:

git clone https://github.com/piroyon/blastweb.git
cd blastweb
pip install -e .

or, use pip:

pip install blastweb

⚙️ Configuration

Create a config file 'blast.yaml' in the current directory

blastweb init

Edit blast.yaml

blast_path: /usr/local/ncbi/blast+/bin
blast_db: /mnt/data/blastdb
default_extra_args: "-soft_masking true -word_size 11"

• blast_path: Path to the directory where blastn, blastp, etc. are installed
• blast_db: Path to the directory containing your BLAST databases
• default_extra_args: Common BLAST options passed to all queries

🚀 Start server for development or very local use

Start the web server:

cd <blastweb_topdir>
blastweb runserver --port 5000 --config /path/to/blast.yaml

Then open http://localhost:5000 in your browser.

🧪 REST API

POST to /api/blast with JSON:

{
  "sequence": "ATGGCGTACGTAGC",
  "program": "blastn",
  "database": "mydb",
  "extra_args": "-word_size 11"
}

Command:

curl -X POST http://localhost:5000/api/blast \
  -H "Content-Type: application/json" \
  -d '{"sequence": "ATGGCGTACGTAGC", "program": "blastn", "database": "mydb"}'

Response (tsv lines split into array of columns):

{
  "results": [["query1", "subject1", "98.7", "123", ...]]
}

🗃️ Custom Databases

Prepare database for BLAST+ with -hash_index & -parse_seqids options.

makeblastdb -in mydb.fa -dbtype [nucl|prot] -hash_index -parse_seqids

Put your databases (e.g. mydb.fa.nin, mydb.fa.nsq, etc.) into the directory specified by blast_db. These will be auto-listed in the form as options.

🔧 Production Deployment with Gunicorn and Nginx

For production environments, it is strongly recommended to run blastweb behind a WSGI server such as gunicorn and use a reverse proxy like nginx to handle TLS, compression, and static file delivery.

Example setup:

[Client] → [nginx :443/80] → [gunicorn :5000] → blastweb.app

Step 1: Install gunicorn

pip install gunicorn

Step 2: Start blastweb with gunicorn

BLASTWEB_CONFIG=/path/to/blast.yaml gunicorn blastweb.wsgi:app --bind 127.0.0.1:5000

Step 3: Configure nginx (external to this project)

a minimal nginx config:

server {
    listen 80;
    server_name your.domain.com;

    location / {
        proxy_pass http://127.0.0.1:5000;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
    }
}

• To enable HTTPS, consider using Let's Encrypt.
• Nginx is not included in this repository — please configure it separately on your server.