def runMain():
### ~ [1] ~ Basic Setup of Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
try:
(info, out, mainlog, cmd_list) = setupProgram()
except SystemExit:
return
except:
print 'Unexpected error during program setup:', sys.exc_info()[0]
return
### ~ [2] ~ Rest of Functionality... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
try: #NewClass(mainlog,cmd_list).run()
print rje_obj.zen(), '\n\n *** No standalone functionality! *** \n\n'
### ~ [3] ~ End ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
except SystemExit:
return # Fork exit etc.
except KeyboardInterrupt:
mainlog.errorLog('User terminated.')
except:
mainlog.errorLog('Fatal error in main %s run.' % info.program)
mainlog.printLog(
'#LOG',
'%s V:%s End: %s\n' % (info.program, info.version,
time.asctime(time.localtime(time.time()))))
def runMain():
### ~ [1] ~ Basic Setup of Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
try: (info,out,mainlog,cmd_list) = setupProgram()
except SystemExit: return
except: print 'Unexpected error during program setup:', sys.exc_info()[0]; return
### ~ [2] ~ Rest of Functionality... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
try:#NewClass(mainlog,cmd_list).run()
print rje_obj.zen(), '\n\n *** No standalone functionality! *** \n\n'
### ~ [3] ~ End ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
except SystemExit: return # Fork exit etc.
except KeyboardInterrupt: mainlog.errorLog('User terminated.')
except: mainlog.errorLog('Fatal error in main %s run.' % info.program)
mainlog.endLog(info)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_HPC', '1.1.1', 'February 2018', '2014')
description = 'High Performance Computing job farming'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_GENOMICS', '0.0.0', 'December 2016', '2016')
description = 'Generic RJE Module'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_Rmd', '0.0.0', 'February 2019', '2019')
description = 'R Markdown generation and execution module'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_EXONERATE', '0.5.0', 'May 2018', '2018')
description = 'Runs Exonerate and parses output'
author = 'Dr Richard J. Edwards & Timothy G. Amos.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('ProtHunter', '0.0.0', 'January 2015', '2015')
description = 'Protein Hunter'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('SLiMDIP', '0.1.0', 'October 2016', '2015')
description = 'Short Linear Motif-Domain Interaction Prediction'
author = 'Richard J. Edwards & Sobia Idrees.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('SeqSuite', '1.8.0', 'May 2015', '2014')
description = 'Miscellaneous biological sequence analysis tools suite'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('TAXMAP', '0.5.0', 'November 2017', '2016')
description = 'Mapping taxonomic groups onto sequences based on Newick trees'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_SPF', '0.1.0', 'April 2016', '2016')
description = 'SPF Level Extraction Tool'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_Taxonomy', '1.3.0', 'June 2018', '2014')
description = 'Downloads, reads and converts Uniprot species codes and NCBI Taxa IDs'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('SLiMParser', '0.5.0', 'September 2017', '2014')
description = 'SLiMSuite REST output parsing tool'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('SLiMSuite', '1.7.1', 'May 2017', '2014')
description = 'Short Linear Motif analysis Suite'
author = 'Dr Richard J. Edwards.'
comments = ['This program is still in development and has not been published.',
'Please see individual programs for citation details.',rje_obj.zen()]
return rje.Info(program,version,last_edit,description,author,time.time(),copy_right,comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('SLiMDIP', '0.1.0',
'October 2016', '2015')
description = 'Short Linear Motif-Domain Interaction Prediction'
author = 'Richard J. Edwards & Sobia Idrees.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copyright) = ('rje_forker', '0.0',
'August 2013', '2013')
description = 'Generic RJE Forking Module'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copyright, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_HPC', '1.1.1',
'February 2018', '2014')
description = 'High Performance Computing job farming'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('Diploidocus', '0.1.0',
'October 2017', '2017')
description = 'In silico diploid data generator.'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_SUPERTREE', '0.2.0',
'June 2018', '2016')
description = 'RJE SuperTree results tidier'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('TAXMAP', '0.5.0',
'November 2017', '2016')
description = 'Mapping taxonomic groups onto sequences based on Newick trees'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('DepthCharge', '0.2.0',
'January 2021', '2021')
description = 'Genome assembly quality control and misassembly repair'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_KAT', '0.0.0',
'September 2021', '2021')
description = 'KAT wrapper and parser'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('SeqSuite', '1.8.0',
'May 2015', '2014')
description = 'Miscellaneous biological sequence analysis tools suite'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('RJE_SPF', '0.1.0',
'April 2016', '2016')
description = 'SPF Level Extraction Tool'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('ProtHunter', '0.0.0',
'January 2015', '2015')
description = 'Protein Hunter'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
def makeInfo(
): ### Makes Info object which stores program details, mainly for initial print to screen.
'''Makes Info object which stores program details, mainly for initial print to screen.'''
(program, version, last_edit, copy_right) = ('SLiMSuite', '1.5.0',
'April 2015', '2014')
description = 'Short Linear Motif analysis Suite'
author = 'Dr Richard J. Edwards.'
comments = [
'This program is still in development and has not been published.',
'Please see individual programs for citation details.',
rje_obj.zen()
]
return rje.Info(program, version, last_edit, description, author,
time.time(), copy_right, comments)
