saavpedia 0.7.2

SAAVpedia python library

# 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,<br/> 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