Welcome to SAAVpedia

What's SAAVpedia

SAAVpedia is a platform for identification, functional annotation, retrieval of single amino-acid variants from proteomic and genomic data.

• SAAVpedia provides three user interfaces consisting of

  • Web User Interface (WUI)
  • Web Application Programming Interface (API)
  • Python package.

• For Users with Python programming skills.

  • This repository offers source codes of SAAVpedia Python package.

• For Users without programming knowledge

  • Use WUI of SAAVpedia - https://www.SAAVpedia.org

Getting Started

[Unix/Linux]

Initial Python Setup for SAAVpedia.

Install SAAVpedia Python at the command prompt if you have not yet:
To install SAAVpedia Python package,
You must have administrator privileges or write-access on Python library folder.

Step One - Install SAAVpedia Python package via PyPI.

$ pip install SAAVpedia   
Collecting SAAVpedia
Downloading https://files.pythonhosted.org/packages/...
Installing collected packages: SAAVpedia
Successfully installed SAAVpedia-x.x.x

Step Two - Upgrade SAAVpedia Python package via PyPI.

$ pip install --upgrade SAAVpedia

Download SAAVpedia DB in the local computer.

$ python
Python 2.7.12 (default, Dec  4 2017, 14:50:18)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from SAAVpedia import SAAVpedia
>>> SAAVpedia().init()
...
Downloading SAAVpedia.sqlite.935.db - 91.23%
Downloading SAAVpedia.sqlite.936.db - 91.33%
Downloading SAAVpedia.sqlite.937.db - 91.42%
...
Generating SAAVpedia DB... - 99.90%
Generating SAAVpedia DB... - 100.00%
Removing temporary files...
SAAVpedia initilzation is completed.
>>> quit()

Install SAAVpedia scripts in the current working directory.

$ python
Python 2.7.12 (default, Dec  4 2017, 14:50:18)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from SAAVpedia import SAAVpedia
>>> SAAVpedia().install()
Copying SAAVinterpreter.py...
Copying SNVretriever.py...
Copying SAAVretriever-Online.py...
Copying SAAVidentifier.py...
Copying SAAVinterpreter-Online.py...
Copying SAAVretriever.py...
Copying SNVretriever-Online.py...
Copying SAAVidentifier-Online.py...

>>> quit()

The list of SAAVpedia command scripts

After installation of SAAVpedia in Python, You can see several SAAVpedia command scripts.

$ ls -l
-rw-r--r-- 1 user user 2333 May 10 09:10 SAAVidentifier-Online.py
-rw-r--r-- 1 user user 2299 May 10 09:10 SAAVidentifier.py
-rw-r--r-- 1 user user 6556 May 10 09:10 SAAVinterpreter-Online.py
-rw-r--r-- 1 user user 6522 May 10 09:10 SAAVinterpreter.py
-rw-r--r-- 1 user user 2328 May 10 09:10 SAAVretriever-Online.py
-rw-r--r-- 1 user user 2294 May 10 09:10 SAAVretriever.py
-rw-r--r-- 1 user user 2326 May 10 09:10 SNVretriever-Online.py
-rw-r--r-- 1 user user 2292 May 10 09:10 SNVretriever.py

Example of Glioma data using SAAVidentifier

$ python SAAVidentifier.py --input Glioma.input.txt 
Reading the input file...
Fetching output data...
Estimated time for fetching data: 0.187811s
Writing "SAAVidentifier-2018-05-10-09h-13m-52.362122s.scf" file...
Total estimated time: 0.230s

Example of Glioma data using SAAVidentifier via online.

$ python SAAVidentifier-Online.py --input Glioma.input.txt 
Reading the input file...
Fetching output data...
Estimated time for fetching data: 1.844199s
Writing "SAAVidentifier-2018-05-10-09h-15m-17.405145s.scf" file...
Total estimated time: 1.883s