https://github.com/gedankenstuecke/entrezfetchr

Small Django project which uses BioPython to fetch Sequences & Publications out of NCBIs Entrez
https://github.com/gedankenstuecke/entrezfetchr

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Small Django project which uses BioPython to fetch Sequences & Publications out of NCBIs Entrez

• Host: GitHub
• URL: https://github.com/gedankenstuecke/entrezfetchr
• Owner: gedankenstuecke
• Created: 2012-06-12T09:19:02.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2012-08-01T17:50:03.000Z (over 12 years ago)
• Last Synced: 2024-06-11T16:26:15.656Z (7 months ago)
• Language: JavaScript
• Size: 188 KB
• Stars: 5
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# EntrezFetchr

A small Django project which uses BioPython to fetch Sequences & Publications out of NCBIs Entrez databases.

Users can upload a list of species they are interested in and provide additional search terms to get back FASTA-formatted sequences out of the nucleotide/protein-database or get a csv-list of publications matching their organisms of interest and the search term. 

## Dependencies

The application makes use of and requires:

* Django (https://www.djangoproject.com/)

* Celery (http://celeryproject.org/)

* RabbitMQ (http://www.rabbitmq.com/)

* Biopython (http://biopython.org/)

## How-To

* Adjust the settings.py to your needs (location of the project, credentials for your SMTP-server, how long results will be saved, maximum number of results per run)

* Run "./manage.py syncdb" to create the SQLite-database for storing celery-results.

* Start your RabbitMQ-server

* Start a Celery-worker: "./manage.py celeryd"

* Fire up the development-server "./manage.py runserver 0.0.0.0:8000"

* Point your browser to localhost:8000 and view the result

## Command-Line-Version

If you do not need the web-stuff and just want to run your search queries from the shell you can use EntrezFetchr.py which is located in /scripts. To use it just pass the script the parameters:

* -i for the species-input-file 

* -s for the search term you are interested in

* -d for the database you want to crawl, right now limited to pubmed, nucleotide and protein

* -e for your email-address, as Entrez requires you to provide contact details to use their database

* -o for the output file

Reminder: You still need Python & Biopython to run the script, but you can skip the Django/RabbitMQ/Celery-dependencies

## Design-Stuff

The CSS is Bootstrap, from Twitter (http://twitter.github.com/bootstrap/)

The icons are Glyphicons Free (http://glyphicons.com/) 

## Contact

If you encounter any bugs or have feature requests feel free to contact me at [email protected] or use the issues at GitHub: https://github.com/gedankenstuecke/EntrezFetchr