build.rna_tools.tools.mq.rna_mq_collect.single_run()

Complexity

Conditions

28

Size

Total Lines	171
Code Lines	94

Duplication

Lines	171
Ratio	100 %

Importance

Changes

0

#!/usr/bin/env python
def single_run(filename):

This code seems to be duplicated in your project.

    """Start a mqaprna run for a given file
    with all methods (according to config file).

    [!] Use global cleanup = False to block cleaning up

    .. warning:: The function uses global variable.
    """
    filename, filename_length = filename
    #print 'fn: ', filename

    global methods, c
    all_results = {}

    for m in methods:
            arguments = ''
            #if DEBUG_MODE: print 'method', m, arguments
            mfull = m
            if verbose: print(m + '...') # show method 'eSCORE...'

The variable verbose does not seem to be defined.

            if m == 'FARNA':
                mfull = m
                arguments = [filename] + [False]

            if m == 'FARNA_hires':
                m = 'FARNA'
                mfull = 'FARNA_hires'
                arguments = [filename] + [True]

            if m == 'FARFAR2':
                m = 'FARFAR2'
                mfull = 'FARFAR2'
                arguments = [filename] + [False]

            if m == 'FARFAR2_hires':
                m = 'FARFAR2'
                mfull = 'FARFAR2_hires'
                arguments = [filename] + [True]
                
            if m == 'RNAkb_all':
                m = 'RNAkb'
                mfull = 'RNAkb_all'
                arguments = [filename] + ['aa']

            if m.find('_') > -1:
                m, n = m.split('_')
                n = n.replace('n', '') # n_XXX
                n = n.replace('k', '000')
                n = n.replace('m', '000000')
                arguments = [filename] + [n]

            if not arguments:
                arguments = [filename] + Config.WRAPPER_OPTIONS[m]

            if m == 'escore':
                m = 'eSCORE'
            wrapper = getattr(MODULES[m], m)()#verbose) # ref_seq, ref_ss, verbose)  # for all wrappers but SSAgrement '','' is OK

            if m == 'NAST_pyro':
                lock.acquire()

The variable lock does not seem to be defined.

            if DEBUG_MODE:
                result = wrapper.run(*arguments)
                if verbose: print(m, result) # ClashScore 12.256669
                all_results[mfull] = result
                if cleanup: wrapper.cleanup()
            else:
                try:
                    result = wrapper.run(*arguments)
                    all_results[mfull] = result
                    if cleanup: wrapper.cleanup()
                except:
                    all_results[mfull] = 'error'
                    if cleanup: wrapper.cleanup()

            # {'ClashScore': 12.256669}
            # {'ClashScore': 12.256669, 'AnalyzeGeometry': 32.5581}
            # {'ClashScore': 12.256669, 'AnalyzeGeometry': 32.5581, 'FARNA': '-20.008,-2.739,-13.175,-77.67,-10.652,-158.51,9.547,8.39,-16.246,-263.281,0.0,0.0,17.782,0.0'}
            #if verbose: print 'all_results:', all_results # this every each method showed

            if m == 'NAST_pyro':
                lock.release()

    # get rmsd
    if opt.native_pdb_filename:

The variable opt does not seem to be defined in case __name__ == '__main__' on line 557 is False. Are you sure this can never be the case?

        rmsd = rmsd_calc.get_rmsd(opt.native_pdb_filename,

The variable rmsd_calc does not seem to be defined.

                                     filename)
        all_results['rmsd'] = rmsd
        methods = methods + ['rmsd']
    else:
        methods = methods

    # length
    length = len(ref_seq)

The variable ref_seq does not seem to be defined.

    all_results['length'] = length

    if opt.mqapscore:
        # meta-score
        ms =  MqapScore(all_results)
        mqap_score = ms.get_score()
        methods = methods + ['SCORE']
        all_results['SCORE'] = mqap_score

    if True:
        lock.acquire()

        global counter_lock
        #with counter_lock:
        counter.value += 1

        if counter.value != 1:
            # @todo does not work
            #sys.stdout.write('\033[F')
            #sys.stdout.write('\033[F')
            pass

        #results = [str(round(all_results[mfull],2)).strip().rjust(9) for m in methods]

        results_str = str(all_results) # "{'AnalyzeGeometry': 0.0, 'eSCORE': 0.10661, 'FARNA': ['-2.411', '0.0', '0.0', '-9.672', '0.0', '-25.678', '0.0', '1.061', '0.0', '-32.098', '0.0', '0.0', '4.601', '0.0'], 'ClashScore': 36.458333, 'length': 0, 'SimRNA_0': ['0', '67.345305', '-37.428', '-23.073', '0.248', '104.524975', '87.955', '9.938', '5.669', '1.089', '-0.126', '', '67.345305'], 'FARNA_hires': ['0.0', '-13.107', '-0.711', '0.0', '5.22', '2.734', '-30.044', '0.223', '-10.511', '-0.173', '-4.719', '1.143', '0.0', '14.371', '9.358'], 'RNAscore': 8.11007, 'RASP': ['-0.1382', '15', '-0.00921333', '-0.0845115', '0.454033', '-0.118248', '-277.666', '949', '-0.292588', '-273.37', '2.51163', '-1.71042', '-584.451', '2144', '-0.272598', '-564.143', '5.77609', '-3.51588', '-1616.08', '6700', '-0.241206', '0', '0', '0'], 'RNAkb': -1}"

        results = [all_results[mfull] for m in methods]

The variable mfull does not seem to be defined in case the for loop on line 190 is not entered. Are you sure this can never be the case?

        # progress bar
        #sys.stdout.write('\r')
        #sys.stdout.flush()
        #sys.stdout.write('\r' + ' ' * 110 + '\r' + filename.split(os.sep)[-1].ljust(50) + ' ' + ' '.join(results))

        ########### line with resluts ######################
        bar.update(counter.value)

The variable bar does not seem to be defined.

        ## my old progress bar here:
        # print(sg.pprogress_line(counter.value, filename_length, ''))# ,
        ## print results, use --verbose now
        if verbose:
            print(filename.split(os.sep)[-1].ljust(20) + ' ' + results_str)
        
        ## [          ]   1 7.14 % 14 3_solution_1.pdb     {'AnalyzeGeometry': 0.0, 'eSCORE': 1.70264, 'FARNA': ['-31.498', '-11.589', '-32.7', '-123.708', '-25.514', '-271.337', '33.563', '2.957', '-36.699', '-471.864', '0.0', '0.0', '24.659', '0.0'], 'ClashScore': 2.201835, 'length': 0, 'SimRNA_0': ['0', '-1016.539381', '-599.475', '-223.162', '-3.935', '-413.129576', '-65.066', '-71.505', '-68.947', '-45.989', '-161.622', '', '-1016.539381'], 'FARNA_hires': ['0.0', '-541.374', '-0.59', '0.0', '1.85', '8.12', '-433.113', '17.811', '-229.203', '3.074', '-140.106', '13.875', '-17.245', '226.762', '7.39'], 'RNAscore': 26.7066, 'RASP': ['-9.3599', '987', '-0.00948318', '8.16333', '3.95157', '-4.4345', '-7976.88', '60547', '-0.131747', '-7274.73', '52.7448', '-13.3123', '-17537.5', '138719', '-0.126424', '-15578.4', '106.602', '-18.3777', '-34270.8', '483436', '-0.07089', '0', '0', '0'], 'RNAkb': -0.019507621989000006}

        #sys.stdout.flush()
        #print
        #sys.stdout.write(sg.pprogress_line(counter.value, filename_length))
        #print sg.pprogress_line(counter.value, filename_length)
        #sys.stdout.flush()

        ## for graphics debugging
        #import time
        #time.sleep(1)

        #format_line([filename.split(os.sep)[-1] + [all_results[m] for m in methods]])  # @todo Nice print with ShellGraphics

        cells = [counter.value, filename.split(os.sep)[-1]] # add id 
        for m in methods:
            if type(all_results[m]) == list:
                cells.extend(all_results[m])
            else:
                cells.append(all_results[m])
        csv_writer.writerow(cells)

The variable csv_writer does not seem to be defined.

        #print 'mqaprna::filename: %i %s' % (counter.value, filename)
        csv_file.flush()

The variable csv_file does not seem to be defined.

        lock.release()

    # hack
    try:
        methods.remove('SCORE')
    except ValueError:
        pass

    try:
        methods.remove('rmsd')
    except ValueError:
        pass