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

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

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

Utilize multiprocessing to speed up your code

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

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:

[APIKEYS]
slack = apikeystring

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

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.