############ Mutation Data Extraction and Aggregation ########### import glob import os import sys sys.path.append("../../common/") ## to analysis/ import config as cf ## some basic shit that I don't want to do myself cf.addpath("run_file_aggregation/") import run_file_aggregation as rf ## aggregate the contents of the tasks.dat file def aggregate_coding_mutations_timeseries(directories, grouping="", subgrouping="", verbose=False, test=False, expected=None): input_files_glob = ["mutation_metrics.csv*" ] ## this is actually a globbing pattern column = 1 outfile = "coding_mutations" return rf.aggregate_timeseries(directories, input_files_glob, outfile, column, grouping=grouping,
################### # Analyze ################### # system includes import glob import os from optparse import OptionParser import sys sys.path.append(os.path.abspath(os.path.join(sys.path[0], "../common/"))) ## to common/ import config as cf cf.addpath("generic/") cf.addpath("fitness/") cf.addpath("modularity/") cf.addpath("coalescence/") cf.addpath("mutations/") cf.addpath("task_ct/") cf.addpath("stats.dat/") cf.addpath("count.dat/") import fitness as fitness import functional_modularity as functional_modularity import coalescence as coalescence import mutations as mutations import task_ct as task_ct import stats_dat as stats_dat import count_dat as count_dat
############ Fitness Data Extraction and Aggregation ########### import glob import os import sys sys.path.append("../../common/") ## to common/ import config as cf## some basic shit that I don't want to do myself cf.addpath( "commongraph/" ) import commongraph as cg ## plot a fitness timeseries def plot_timeseries( grouping="", subgrouping="" ): input_files_glob = "*fitness.timeseries.csv" ## this is actually a globbing pattern outfile = "fitness" legend = True datasources = 1 ## this is weird, but an artifact of plot_from_csv. bar_chart_from_csv is more sane. title = "Fitness by Treatment" xlabel = "Updates" ylabel = "Fitness" ploterror = True xtickinterval = 50 ## maybe make this saner or configurable at some point, but all my stuff is this right now type = "median_only" return cg.plot_timeseries( input_files_glob, outfile, grouping=grouping, subgrouping=subgrouping, legend=legend,
############ Tasks Count Data Extraction and Aggregation ########### import glob import os import sys sys.path.append("../../common/") ## to analysis/ import config as cf## some basic shit that I don't want to do myself cf.addpath( "run_file_aggregation/" ) import run_file_aggregation as rf ## aggregate the contents of the tasks.dat file def aggregate_timeseries( directories, grouping="", subgrouping="", verbose=False, test=False, expected=None ): input_files_glob = ["tasks.dat*"] ## this is actually a globbing pattern column = 3 outfile = "task_ct" return rf.aggregate_timeseries( directories, input_files_glob, outfile, column, grouping=grouping, subgrouping=subgrouping, verbose=verbose, test=test, expected=expected )
############ Task Count Data Plotting ########### import glob import os import sys sys.path.append("../../common/") ## to common/ import config as cf ## some basic shit that I don't want to do myself cf.addpath("commongraph/") import commongraph as cg ## plot a fitness timeseries def plot_timeseries(grouping="", subgrouping=""): input_files_glob = "*task_ct.timeseries.csv" ## this is actually a globbing pattern outfile = "task_ct" legend = True datasources = 1 ## this is weird, but an artifact of plot_from_csv. bar_chart_from_csv is more sane. title = "Task Count by Treatment" xlabel = "Updates" ylabel = "Task Count" ploterror = True xtickinterval = 50 ## maybe make this saner or configurable at some point, but all my stuff is this right now type = "median_only" return cg.plot_timeseries(input_files_glob, outfile, grouping=grouping, subgrouping=subgrouping, legend=legend,
############ Run File Data Extraction and Aggregation ########### import glob import os import sys sys.path.append("../../common/") ## to analysis/ import config as cf## some basic shit that I don't want to do myself cf.addpath( "integrity_testing/" ) import integrity_testing as it extract_single_column_to_csv_path = cf.getpath( "common/extract_single_column_to_csv.py" ) aggregate_file_path = cf.getpath( "common/aggregate_file.py" ) def aggregate_timeseries( directories, input_files_glob, outfile, column, grouping="", subgrouping="", verbose=False, separator=" ", header=False, test=False, expected=None ): cwd = cf.Config.Script.cwd if grouping: grouping = "%s_" % grouping if subgrouping: subgrouping = "%s__" % subgrouping headeropt = "" if header: headeropt = "--header" aggregate_filename = os.path.join( cwd, "%s%s%s.timeseries.csv" % (grouping, subgrouping, outfile) ) if test:
#!/usr/bin/python ################### # Analyze ################### # system includes import glob import os from optparse import OptionParser import sys sys.path.append( os.path.abspath( os.path.join( sys.path[0], "../common/" ) ) ) ## to common/ import config as cf cf.addpath( "generic/" ) cf.addpath( "fitness/" ) cf.addpath( "modularity/" ) cf.addpath( "coalescence/" ) cf.addpath( "mutations/" ) cf.addpath( "task_ct/" ) cf.addpath( "stats.dat/" ) cf.addpath( "count.dat/" ) import fitness as fitness import functional_modularity as functional_modularity import coalescence as coalescence import mutations as mutations import task_ct as task_ct import stats_dat as stats_dat import count_dat as count_dat
################### # Make Graphs ################### # system includes import glob import os from optparse import OptionParser import sys sys.path.append( os.path.abspath( os.path.join( sys.path[0], "../common/" ) ) ) ## to common/ #print sys.path import config as cf cf.addpath( "fitness/" ) #cf.addpath( "modularity/" ) #cf.addpath( "coalescence/" ) #cf.addpath( "mutations/" ) cf.addpath( "task_ct/" ) cf.addpath( "stats.dat/" ) cf.addpath( "count.dat/" ) import fitness as fitness import task_ct as task_ct #import functional_modularity as functional_modularity #import coalescence as coalescence #import mutations as mutations import stats_dat as stats_dat import count_dat as count_dat
################### # Make Graphs ################### # system includes import glob import os from optparse import OptionParser import sys sys.path.append(os.path.abspath(os.path.join(sys.path[0], "../common/"))) ## to common/ #print sys.path import config as cf cf.addpath("fitness/") #cf.addpath( "modularity/" ) #cf.addpath( "coalescence/" ) #cf.addpath( "mutations/" ) cf.addpath("task_ct/") cf.addpath("stats.dat/") cf.addpath("count.dat/") import fitness as fitness import task_ct as task_ct #import functional_modularity as functional_modularity #import coalescence as coalescence #import mutations as mutations import stats_dat as stats_dat import count_dat as count_dat