LogIt Documentation

Use the LogIt class to make logging very simple. This short and sweet class wraps around logzero which allows color coded logging. We created our own default logger with a default dateformat, logformat, and logging level (default is debug).

Note that LogIt automaticall capitalizes the logname.

  1. Import the LogIt class and create a variable. ex: logit = LogIt()
  2. Create your logger. ex: blastn = logit.default('blastn', 'blastn.log')
  3. Start logging. ex: blastn.error('Your refseq accession was not found')

Multiple loggers can exist for the same logfile and multiple loggers can be set up for one script which is shown in the example below.


Simple logging

from OrthoEvol.Tools import LogIt
genbank_log = LogIt().default(logname="genbank", logfile=None)

Use logging with ETE3PAML

from OrthoEvol.Tools import LogIt
from OrthoEvol.Orthologs.Phylogenetics import ETE3PAML

# Set up your loggers
logit = LogIt()

# Log to one file
logfile = 'align2paml.log'

align, paml = logit.default('alignlog', logfile), logit.default('pamllog', logfile)

# Start logging

# Shutdown the loggers and delete the logfile

# Shutdown logging without deleting the logfile