semvec/pypi-packages huggingface dataset:
blast-score-ratio 1.0.6
Get BLAST Score Ratios (BSR; as described in Rasko et al (2006) doi:10.1186/1471-2105-6-2)

Obtain BLAST score ratios (BSRs), for use in comparative genomics and
identifying horizontally transferred genetic material, from fastA files
containing the protein sequences for different organisms.

BSR (Rasko et al, 2006) is obtained by running BLAST using a reference proteome
against one or more other proteomes. The highest BLAST score for each reference
sequence is normalised by dividing by the score for 100% match to the reference
sequence. This analysis can identify shared genetic material in unrelated
strains or species, and find genes unique to a particular strain, for example.

A series of BLAST are performed and objects are created for each reference
sequence containing the results of the analysis. Charts showing relative BSR
in the form of a 2-D graph, histogram and heatmap can be quickly generated.

This program should be run from within the Python environment using
blast_score_ratio.bsr.get_bsr(*args). All functions and classes are fully
documented. The best way to understand how this works is to look at demo.py
for an example project.

Example:
    import blast_score_ratio.bsr as bsr
    bsr.test()

Requires NCBI BLAST+ command line >=2.2.29 application available here:
    ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
BLAST binaries must be in your computer's path.
Also requires biopython and matplotlib packages.

tested with python v3.6.0, biopython v1.68, matplotlib v2.0.0 on Windows 10
synerty-peek 0.5.0.1
Peek Platform - Meta Package to install all services
Keywords: Peek,Python,Platform,synerty

.. image:: https://readthedocs.org/projects/synerty-peek/badge/?version=latest
    :target: http://synerty-peek.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

============
Synerty Peek
============

What is Peek
------------

Peek is semi distributed pluggable python platform.

Peek provides a platform for Python similar to the functionality JBOSS provides for JAVA.
(Or at least that is in the intention, it's early days)

The Big Bang
------------

Peek was created and is maintained by Synerty to be a distributed, pluggable
python platform that provides many of the core services needed for enterprise applications.

We wanted to integrate smaller peices of code, that can leverage different existing
boilerplate code which the platform provides. For example,
services for parallel processing or services for business integrations.

The Peek Platform allows developers to better write and integrate smaller units of code.

Synerty uses the Peek platform to provide scalable enterprise grade applications to the
power utilities sector.

Cross Platform
--------------

Peek is compatible with the following operating systems

*   Linux (Preferred)

    *   Debian 8
    *   Redhat Enterprise Linux 6+

*   Windows (64bit only)

    *   Windows 7
    *   Windows 10
    *   Windows 2008R2
    *   Windows 2012R2

Technologies
------------

The Peek Platform is integrated with some fantastic technologies, here is a run down:

*   Reactive / observable data transport, using:

    *   Synerty VortexPY, VortexJS
        (Synerty's observable, routable, data serialisation and transport library)
    *   RxPY

*   Reactive framework, using:

    *   Twisted

*   A web based user and admin site, using:

    *   Bootstrap3
    *   Angular2+, Angular CLI
    *   Typescript
    *   FontAwesome
    *   Web Sockets with HTTP Fallback

*   A native mobile app, using:

    *   Nativescript2+
    *   Angular2+
    *   Typescript
    *   FontAwesome
    *   Web Sockets

*   Persistent Storage, using:

    *   Alembic
    *   SQLAlchemy
    *   PostGreSQL (NoSQL and SQL) (Preferred), or
    *   MS SQL Server (SQL Only)

*   Multiprocessing worker services, using:

    *   Celery
    *   rabbitmq
    *   redis

*   External data input / output (EG, External SQL or SOAP), for example:

    *   SOAPpy
    *   txSuds
    *   cxOracle
    *   Any other libraries your plugins wants to install


Browser Support
---------------

Peek provides two separate web apps, one for administration, and one for users.
These web applications are tested against the following browsers.

Current Browser Support
```````````````````````
*   Desktop

    *   Chrome
    *   IE 11 and above
    *   Microsoft Edge
    *   Safari on Mac

*   Mobile

    *   Safari on iOS
    *   Mobile Chrome

How to Use Peek Documention
---------------------------

The Peek platform documentation is designed like code (IE, Modular).

http://synerty-peek.readthedocs.io/

.. image:: ./README_doc_map.png
peek-admin 0.5.0
Peek Platform - Admin Service (Frontend)
Keywords: Peek,Python,Platform,synerty

=============================
Peek Platform - Admin Service
=============================

The Peek Admin service contains the Angular Web build environment.

The frontend is for typescript + bootstrap3 + angular2

Development
-----------

Web Frontend
````````````

The frontend is compiled/built from the backend python software when it starts. The python
backend then serves up the the webpack bundles. This is accessible via http://<ip>:8010

When you are developing with the frontend, you can start it in development mode

::

        cd <project dir>/peek_admin/build-web
        npm start

This will start a NODE development server. It will watch the project files, rebuild the
project and live reload the browser when you make changes.
It's accessed via http://<ip>:4200

There is a proxy.conf.json file that is configured to pass through certain resources to
the backend server. This allows the NODE development server to hand handle all the assets
and the backend to still handle the file uploads, vortex, etc.
peek-mobile 0.5.0
Peek Platform - Mobile Service (Frontend)
Keywords: Peek,Python,Platform,synerty

==============================
Peek Platform - Mobile Service
==============================

The Peek Mobile service contains the Angular Web and Nativescript build environments.

The frontend is for typescript + bootstrap3 + angular2

Development
-----------

Web Frontend
````````````

The frontend is compiled/built from the backend python software when it starts. The python
backend then serves up the the webpack bundles. This is accessible via http://<ip>:8000

When you are developing with the frontend for Web, you can start development mode with:

::

        cd <project dir>/peek_mobile/build-web
        npm start


This will start a NODE development server. It will watch the project files, rebuild the
project and live reload the browser when you make changes.
It's accessed via http://<ip>:4200

There is a proxy.conf.json file that is configured to pass through certain resources to
the backend server. This allows the NODE development server to hand handle all the assets
and the backend to still handle the file uploads, vortex, etc.

NativeScript
````````````

When you are developing for NativeScript, you can build and start the app with:

::

        cd <project dir>/peek_mobile/build-ns
        tns run <platform> --watch
peek-worker 0.5.0
Peek Platform - Worker Service
Keywords: Peek,Python,Platform,synerty

==============================
Peek Platform - Worker Service
==============================

The Peek Worker service provides peek apps with distributed multiprocessing support.
This is provided with Celery.

See http://www.celeryproject.org

.#  Ability to farm out computationally expensive tasks to a cluster, or at least
    multiple threads.

.#  The workers get their own connection to the DB in their own fork.