Пример #1
0
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()))))
Пример #2
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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)
Пример #3
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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)
Пример #4
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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)
Пример #5
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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)
Пример #6
0
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)
Пример #7
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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)
Пример #8
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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)
Пример #9
0
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)
Пример #10
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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)
Пример #11
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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)
Пример #12
0
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)
Пример #13
0
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)
Пример #14
0
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)
Пример #15
0
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)
Пример #16
0
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)
Пример #17
0
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)
Пример #18
0
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)
Пример #19
0
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)
Пример #20
0
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)
Пример #21
0
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)
Пример #22
0
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)
Пример #23
0
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)
Пример #24
0
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)
Пример #25
0
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)
Пример #26
0
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)