saavpedia

# 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

Release files for saavpedia 0.7.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Built distribution (wheel)

Table of built distributions (wheels) for saavpedia 0.7.2
File	Interpreter	ABI	Platform	Reset
SAAVpedia-0.7.2-py2-none-any.whl 40.2 kB May 29, 2018	Python 2	none	any	Details

Release files / SAAVpedia-0.7.2-py2-none-any.whl

Download URL	SAAVpedia-0.7.2-py2-none-any.whl
Size	40.2 kB
Tags	Python 2
SHA-256 checksum How to use checksums	`0aed16675927bb5e057554a1ac15e2ab3ca8ccfb3b515dcdab278d74e197f6d2`
BLAKE2b-256 checksum How to use checksums	`46770895b1cabaa4d3c215c8307df7b815b1e94c88c9cde23f3356b771c3dba6`
Upload date	May 29, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No