saavpedia 0.4.8.0

# Welcome to SAAVpedia

### SAAVpedia: identification, functional annotation, retrieval of single amino-acid variants from proteomic and genomic data.

## 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**, **Web API** and **Python package**.
* Web User Interface for users without programming knowledge
* Visit https://www.SAAVpedia.org
* This GitHub repository has source codes of SAAVpedia Python package.


## Getting Started
1. 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.
#### [Unix/Linux]
##### Install SAAVpedia Python package via PyPI.
$ pip install SAAVpedia
Collecting SAAVpedia
Downloading https://files.pythonhosted.org/packages/57/e6/.../SAAVpedia-1.0.0-py2-none-any.whl
Installing collected packages: SAAVpedia
Successfully installed SAAVpedia-1.0.0

##### 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().install()
...
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.
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

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