Contains revised General Object templates for Rich Edwards scripts and bioinformatics programs
Copyright © 2011 Richard J. Edwards - See source code for GNU License Notice
This module contains updated Classes for use by all RJE scripts and bioinformatics programs. With time, all programs should be migrated over to the new objects. Miscellaneous methods will, for the most part, be kept in the rje module.
History Module Version History
# 0.0 - Initial Compilation based on rje.py objects. # 1.0 - Fully working version, so upgraded to 1.0. Added dev and warn options. # 1.1 - Added rje_zen import and self.zen() to call rje_zen.Zen().wisdom(). # 1.2 - Added warnLog functions. # 1.3 - Added perc cmdtype = float that is multiplied by 100.0 if < 1.0. Also added cmdtype = date for YYYY-MM-DD. # 1.4 - Added sourceDataFile() method from SLiMBench for wider use. # 1.5 - Added 'basefile' cmdlist types. # 1.6 - Added osx=T/F option for Mac-specific running options. # 1.7 - Added self.name() to basic object class. # 1.8 - Cleaned up some erroeneous opt, stat and info references. # 2.0 - Added self.file dictionary and methods for handling file handles with matching self.str filenames. # 2.1.0 - Added new built-in attributes/options for REST services. # 2.1.1 - Removed excess REST HTML methods. # 2.1.2 - Tweaked glist cmdRead warnings. # 2.1.3 - Modified integer commands to read/convert floats. # 2.2.0 - Added screenwrap=X. # 2.2.1 - Improved handling of integer parameters when given bad commands. # 2.2.2 - Updated error handling for full REST output. # 2.3.0 - Added quiet mode to object and stderr output. # 2.4.0 - Added vLog() and bugLog() methods. # 2.4.1 - Fixed bug where silent=T wasn't running silent. # 2.5.0 - Added flist command type that reads file lines as a list, ignoring commas. # 2.5.1 - Started updated formatting for Python3 compatibility. # 2.6.0 - Added threads() method to basic object. # 2.7.0 - Added loggedSystemCall() # 2.7.1 - Fixed formatting for Python 2.6 back compatibility for servers. # 2.7.2 - Tweaked the forks and threads settings and methods. # 2.7.3 - Added generic checkForProgram() method. # 2.8.0 - Added recognition of -cmd=ARG arguments. # 2.8.1 - Fixed ignoredate bug. # 2.9.0 - Expanded checkForProgram() method to
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