Tools Documentation
===================

The Tools module is a collection of often used classes or functions that
either enhance our other modules and create reusable functions to be
used in various modules.

We’ve incorporated tools for sge tools for use with pbs, a pandoc script
and class for converting docx files to markdown formats, multiprocessing
in multiprocess, and a ftp module that aids in downloading files from
NCBI’s ftp repository.

Examples
--------

Take a look at the examples below to get an idea of how to incorporate
these tools in your project and how we use these tools in our project.

Download NCBI databases with our NCBI FTP Client
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

   from OrthoEvol.Tools.ftp import NcbiFTPClient

   ncbiftp = NcbiFTPClient(email='somebody@gmail.com')
   ncbiftp.getblastdb(database_name='refseq_rna')

List all subdirectories in a NCBI FTP Path
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python


   ncbiftp.listdirectories(path='/blast/db/')
   Out[54]: ['FASTA', 'cloud']

Utilize multiprocessing to speed up your code
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

   from OrthoEvol.Tools.parallel import Multiprocess


   def printwords(word):
       print(word)


   words = ['bae', 'luh', 'cuh']

   if __name__ == '__main__':
       mp = Multiprocess()
       mp.map2function(printwords, words)

Integrate logging in a simple and quick way
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

   from OrthoEvol.Tools.logit import LogIt

   # Set up your loggers
   logit = LogIt().default(logname='test1 log', logfile='log.txt')

   # Shutdown logging without deleting the logfile
   logit.shutdown()

Send a message to a slack channel
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Your config file should look as such:

.. code:: python

   [APIKEYS]
   slack = apikeystring

.. code:: python

   from OrthoEvol.Tools.slackify import Slackify

   slack = Slackify(slackconfig='path/to/slackconfig.cfg')
   message_to_channel = 'Hey, <@username>. This is an update for the current script.'

   slack.send_msg(channel='channelname', message=message_to_channel)

Importing all tools modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

   from OrthoEvol.Tools.ftp import BaseFTPClient, NcbiFTPClient
   from OrthoEvol.Tools.logit import LogIt
   from OrthoEvol.Tools.mygene import MyGene
   from OrthoEvol.Tools.parallel import Multiprocess
   # from OrthoEvol.Tools.pandoc import PandocConverter
   from OrthoEvol.Tools.send2server import S2S
   from OrthoEvol.Tools.sge import (BaseSGEJob, SGEJob, Qstat, SGEPipelineTask,
                                    randomid, basejobids, import_temp,
                                    writecodefile,
                                    file2str)
   from OrthoEvol.Tools.slackify import Slackify

Additional Documentation
------------------------

Check the specific modules for more detailed readmes and examples of
using the tools with this package.