Package: saavpedia
# Welcome to SAAVpedia## What’s SAAVpedia
####SAAVpediais a platform foridentification, functional annotation, retrieval of single amino-acid variants from proteomic and genomic data.
-SAAVpedia providesthree user interfaces consisting ofWeb 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,<br/>
Youmust have administrator privilegesorwrite-accesson Python library folder.##### Step One - Install SAAVpedia Python package via PyPI.$ pip install SAAVpedia
Collecting SAAVpedia
Downloadinghttps://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