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 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 import LogIt

# Set up your loggers
logit = LogIt()

# Log to one file
logfile = 'test.log'

test1 = logit.default('test1 log', logfile)

# Start logging
test1.info('hi')

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

Additional Documentation¶

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