Skip to main content

SAAVpedia python library

Project description

# 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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for saavpedia, version 0.7.2
Filename, size File type Python version Upload date Hashes
Filename, size SAAVpedia-0.7.2-py2-none-any.whl (40.2 kB) File type Wheel Python version py2 Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page