semvec/pypi-packages huggingface dataset:
korbinian 0.3.4
Bioinformatic sequence analysis of membrane proteins.
License: MIT
Keywords: bioinformatics protein sequence membrane conservation evolution membranous soluble polypeptide BLAST SIMAP

korbinian
=========

Bioinformatic sequence analysis of membrane proteins.

What is this repository for?
----------------------------

* Parsing of UniProt flatfiles
* Downloading homologues (primarily with SIMAP)
* Parsing BLAST-like XML files
* Analysis of protein sequences
* Automated figure creation

License
-------

* korbinian is released under the permissive MIT licence

Credits
-------

* Mark Teese
* Martin Ortner
* Shenger Wang
* Rimma Jenske
* Enzo Torasso
* Dominik Mueller

Citation
--------

* scientific publication to be added
* currently cited as "the korbinian python package (Mark Teese, Technical University of Munich)"

Contact
-------
For contact details, see the image below. 


Further contact details are available at my `staff page`__ within the `Langosch lab`__
of the Technical University of Munich.

.. _StaffPage: http://cbp.wzw.tum.de/index.php?id=49&L=1
.. _LangoschPage: http://cbp.wzw.tum.de/index.php?id=9

__ StaffPage_
__ LangoschPage_


.. image:: https://raw.githubusercontent.com/teese/eccpy/master/docs/images/signac_seine_bei_samois.png
   :height: 150px
   :width: 250px

Example Summary Files
---------------------

.. image:: https://raw.githubusercontent.com/teese/korbinian/master/korbinian/examples/images/density.png
   :height: 600 px
   :width: 600 px

Compare three different membrane protein families:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. image:: https://raw.githubusercontent.com/teese/korbinian/master/korbinian/examples/images/n_homol.png
   :height: 500 px
   :width: 700 px

.. image:: https://raw.githubusercontent.com/teese/korbinian/master/korbinian/examples/images/aa_propens.png
   :height: 500 px
   :width: 700 px

.. image:: https://raw.githubusercontent.com/teese/korbinian/master/korbinian/examples/images/len.png
   :height: 500 px
   :width: 700 px

.. image:: https://raw.githubusercontent.com/teese/korbinian/master/korbinian/examples/images/percent_TM.png
   :height: 500 px
   :width: 700 px
pytoxr 0.0.7
Tools for the analysis of data from ToxR experiments.
License: MIT
Keywords: ToxR transmembrane TOXCAT TMDhomodimer GALLEX AraTM BacTH

pytoxr
======

Open-source ToxR data analysis.

Transmembrane-domain interactions of proteins are vital for cellular function. 
ToxR, TOXCAT and dsTBL are powerful tools for investigating these interactions in natural membrane environment. 
The pytoxr module contains tools for the analysis of data from ToxR-based laboratory experiments.

Installation
------------
::

	pip install pytoxr

pytoxr requires python (tested for 3.x) with the standard scientific packages numpy, scipy, pandas, seaborn, and matplotlib.
Pip should also automatically install the eccpy package of Mark Teese (https://github.com/teese/eccpy).

Development Status
------------------

pytoxr has been used to analyse a small number of data files within our work group. 
Code is available to use without any guarantee or warranty. It has not been extensively tested.

Citation
--------

A peer-reviewed article is in preparation. 
For now, please reference as the "pytoxr package of Mark Teese, Technical University of Munich."

License
-------
This software is released under the permissive MIT license.

Contact
-------
For contact details, see the image below. 


Further contact details are available at my `staff page`__ within the `Langosch lab`__
of the Technical University of Munich.

.. _StaffPage: http://cbp.wzw.tum.de/index.php?id=49&L=1
.. _LangoschPage: http://cbp.wzw.tum.de/index.php?id=9

__ StaffPage_
__ LangoschPage_


.. image:: https://raw.githubusercontent.com/teese/eccpy/master/docs/images/signac_seine_bei_samois.png
   :height: 150px
   :width: 250px
ldap-tools 0.7.12
A set of tools to make managing LDAP users, groups, and keys easier
License: MIT

LDAP Tools
==========

This LDAP tools gem is designed as a wrapper around `ldap3` to make
interacting with LDAP easier. No knowledge of LDIF required.


+ Requirements_
+ Installation_

  * `Installation from pypi`_
  * `Installation from source`_

+ Configuration_

  * ldap_info.yaml_
  * ldap.secret_

+ Commands_

  * ldaptools_

    - `Currently supported subcommands`_

Requirements
------------

Use `pyenv` to install python 3.5.3 (or 3.6.4)

The following items are installed automatically as part of the pip install:
- ldap3
- click
- sshpubkeys
- pyyaml

Installation
------------

Installation from pypi
~~~~~~~~~~~~~~~~~~~~~~~~

::

    pip install ldap-tools

Installation from source
~~~~~~~~~~~~~~~~~~~~~~~~

::

    pip install git+https://github.com/carta/ldap_tools#egg=ldap_tools

Configuration
-------------

There are two files used by this application. The default location is
`$HOME/.ldap`; however, this can be overridden using the `LDAP_CONFIG_DIR`
environment variable

ldap_info.yaml
~~~~~~~~~~~~~~

This config file provides basic information about your LDAP server
setup.

.. code:: yaml

    ---
    server: # LDAP server
    user_dn: # DN of user to interact with LDAP
    port: # LDAP port
    basedn: #LDAP Base DN
    mail_domain: # Domain to be used for user email addresses
    service_ou: # Organization Unit (OU) for service accounts

Note: DN of a user is the unique name used to identify that user


ldap.secret
~~~~~~~~~~~

This is a base64-encoded file with the LDAP root password.

Commands
--------

ldaptools
~~~~~~~~~

This is the base command from which all other commands are launched

::

    Usage: ldaptools [OPTIONS] COMMAND [ARGS]...

    Enter the application here.

    Options:
      --help  Show this message and exit.

    Commands:
      audit    Display LDAP group membership by user, by...
      group    LDAP Group Management Commands.
      key      Manage LDAP user SSH public keys.
      user     LDAP User Management Commands.
      version  LDAP Group Management Commands.

Help is available for all subcommands in a similar fashion.

Currently supported subcommands
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  user create
-  user delete
-  group create
-  group delete
-  group add_user
-  group remove_user
-  key add
-  key remove
-  key install
-  audit by_user
-  audit by_group
-  audit raw

Changelog
=========


(unreleased)
------------
- Update changelog. [Ali Tayarani]
- Bump version: 0.7.11 → 0.7.12. [Ali Tayarani]
- Update dependencies. [Ali Tayarani]


v0.7.11 (2018-05-09)
--------------------
- Initial commit. [Ali Tayarani]