saavpedia

# 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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Metadata

Release files for saavpedia 0.4.7.2

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 0.4.7.2
File	Interpreter	ABI	Platform	Reset
SAAVpedia-0.4.7.2-py2-none-any.whl 34.1 kB May 17, 2018	Python 2	none	any	Details

Release files / SAAVpedia-0.4.7.2-py2-none-any.whl

Download URL	SAAVpedia-0.4.7.2-py2-none-any.whl
Size	34.1 kB
Tags	Python 2
SHA-256 checksum How to use checksums	`7be76672e5bffd90478930186254a2da417ea64ff4c4ea31c5a94b5d7979ca87`
BLAKE2b-256 checksum How to use checksums	`4d24e3d6313324757dfbad1eb8129aa224b6723669d96c151a4e68027f1b9c79`
Upload date	May 17, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No