https://github.com/abdelhak-zaaim/bioblastautomation
bioBlastAutomation is a Python-based project designed to automate the process of performing BLAST search .
https://github.com/abdelhak-zaaim/bioblastautomation
automation biology biopython blast django ncbi
Last synced: 7 months ago
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bioBlastAutomation is a Python-based project designed to automate the process of performing BLAST search .
- Host: GitHub
- URL: https://github.com/abdelhak-zaaim/bioblastautomation
- Owner: abdelhak-zaaim
- License: mit
- Created: 2024-03-30T20:45:57.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-04-19T22:52:35.000Z (over 1 year ago)
- Last Synced: 2024-05-02T04:22:35.148Z (over 1 year ago)
- Topics: automation, biology, biopython, blast, django, ncbi
- Language: CSS
- Homepage:
- Size: 870 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# bioBlastAutomation :rocket:
`bioBlastAutomation` is a Python-based project designed to automate the process of performing BLAST (Basic Local Alignment Search Tool) operations. BLAST is a bioinformatics algorithm used to compare primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
This project utilizes the Biopython library, a set of tools for biological computation, and django, a web framework for Python. It also employs Plotly for data visualization.
The `bioBlastAutomation` project includes utilities for validating and identifying the type of sequences (DNA, RNA, Protein) and for checking the compatibility of the sequence with the BLAST program. It also includes functionality for saving BLAST results in different formats (XML, JSON, CSV).
A unique feature of this project is its web interface, which displays a bar chart of sequence alignments. These alignments are read from a file and visualized using Plotly.
The project is managed with pip and has dependencies on several libraries, as listed in the `requirements.txt` file.
## Installation :wrench:
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
```bash
# Clone the repository
git clone https://github.com/abdelhak-zaaim/BioBlastAutomation.git
# Navigate to the project directory
cd BioBlastAutomation
# Install the required packages
pip install -r requirements.txt
```
1. Apply the migrations by executing the commands
```bash
python manage.py makemigrations
python manage.py migrate
```
2. Run the application by executing the command (web interface)
```bash
python manage.py runserver
```
## finaly you can access the web interface by visiting the url its shown in the terminal
