def main(args): verbose = args.verbose #directory = assemblePath(args.input,'summary') directory = args.input msg = 'AMiGA is peeking inside the summary directory' smartPrint('',verbose) smartPrint(tidyMessage(msg),verbose) # smartPrint(checkDirectoryNotEmpty(directory,'Summary')[1],verbose) criteria = checkParameterCommand(args.subset,sep=',') directory,filename = isFileOrFolder(directory,up=1) if filename: ls_files = ['{}{}{}'.format(directory,os.sep,filename)] else: ls_files = findPlateReaderFiles(directory,'.txt') full_df = read(ls_files) sub_df = subsetDf(full_df,criteria) sub_df = group(sub_df,args) sub_df = pivot(sub_df,args,args.value) sub_df = reduceDf(sub_df,args) clusterMap(sub_df,full_df,args,directory) saveDf(full_df,sub_df,args,directory)
def main(): args = parseCommand() verbose = args['verbose'] #directory = assemblePath(args['fi'],'summary') directory = args['fi'] msg = 'AMiGA is peeking inside the summary directory' smartPrint('', verbose) smartPrint(tidyMessage(msg), verbose) # smartPrint(checkDirectoryNotEmpty(directory,'Summary')[1],verbose) criteria = checkParameterCommand(args['s'], sep=',') directory, filename = isFileOrFolder(directory, up=1) if filename: ls_files = ['{}{}{}'.format(directory, os.sep, filename)] else: ls_files = findPlateReaderFiles(directory, '.txt') df = read(ls_files) df = subsetDf(df, criteria) df = group(df, args) df = pivot(df, args) df = reduceDf(df, args) #plot(df,args,directory) clusterMap(df, args, directory)
def main(args): verbose = args.verbose directory = args.input ovewrrite = args.over_write msg = 'AMiGA is parsing your file(s)' smartPrint('',verbose) smartPrint(tidyMessage(msg),verbose) directory,filename = isFileOrFolder(directory,up=1) if filename: ls_files = ['{}{}{}'.format(directory,os.sep,filename)] else: ls_files = findPlateReaderFiles(directory,'.txt') for lf in ls_files: df = read(ls_files) if ovewrrite: new_name = lf elif lf.endswith('.txt'): new_name = '{}_normalized.txt'.format(lf[:-4]) else: new_name = '{}.normalized.txt'.format(lf) df = normalizeParameters(args,df) df.to_csv(new_name,sep='\t',header=True,index=True) msg = 'AMiGA compelted your request' smartPrint('',verbose) smartPrint(tidyMessage(msg),verbose)
def __init__(self, args, config=config): # parse terminal command for arguments #args = parseCommand(args,config); # did the user provide a path that points to a file or directory? parent, filename = isFileOrFolder(args.input) # communicate with user print() print(tidyMessage('AMiGA is peeking inside the working directory')) # define file paths for AMiGA-relevant folders (dict) directory = mapDirectories(parent) # define file paths for AMiGA-relevant files (dict) files = mapFiles(directory) # validate working directory structure and contents (no output) validateDirectories(directory, verbose=args.verbose) # communicate with user print( tidyMessage( 'AMiGA is parsing command-line arguments and parameter files')) # interpret terminal command or text files for parameters (dict) params, args = interpretParameters(files, args, verbose=args.verbose) # communicate with user print(tidyMessage('AMiGA is parsing and cleaning data files')) # parse data files (dict) data = readPlateReaderFolder(filename, directory, interval=params['interval'], save=args.save_cleaned_data, verbose=args.verbose) # communicate with user print(tidyMessage('AMiGA is parsing and reading mapping files')) # parse mapping files and mapping data (dict) mappings = assembleMappings(data, directory['mapping'], files['meta'], save=args.save_mapping_tables, verbose=args.verbose) self.directory = directory self.params = params self.args = args self.data = data self.mappings = mappings
def main(args): verbose = args.verbose directory = args.input overwrite = args.over_write confidence = float(args.confidence) / 100.0 z_value = (1 - (1 - confidence) / 2) add_noise = args.include_noise msg = 'AMiGA is parsing your file(s)' smartPrint('', verbose) smartPrint(tidyMessage(msg), verbose) directory, filename = isFileOrFolder(directory, up=1) # packge filename(s) into a list if filename: ls_files = ['{}{}{}'.format(directory, os.sep, filename)] else: ls_files = filename for lf in ls_files: df = pd.read_csv(lf, sep='\t', header=0, index_col=0) # define file name for the updated dataframe if overwrite: new_name = lf elif lf.endswith('.txt'): new_name = '{}_confidence.txt'.format(lf[:-4]) else: new_name = '{}_confidence.txt'.format(lf) # compute confidecne intervals and save results if args.type == 'Parameters': df = get_parameter_confidence(df, z_value) df.to_csv(new_name, sep='\t', header=True, index=True) elif args.type == 'Curves': df = get_curve_confidence(df, z_value, add_noise) df.to_csv(new_name, sep='\t', header=True, index=False)
from libs.analyze import basicSummaryOnly, runGrowthFitting, runCombinedGrowthFitting from libs.comm import tidyMessage from libs.config import config from libs.detail import assembleMappings from libs.interface import parseCommand, interpretParameters from libs.org import isFileOrFolder, mapDirectories, mapFiles, validateDirectories from libs.read import readPlateReaderFolder from libs.test import HypothesisTest from libs.trim import trimInput # parse terminal command for arguments args = parseCommand(config) # did the user provide a path that points to a file or directory? parent, filename = isFileOrFolder(args['fpath']) # communicate with user print() print(tidyMessage('AMiGA is peeking inside the working directory')) # define file paths for AMiGA-relevant folders (dict) directory = mapDirectories(parent) # define file paths for AMiGA-relevant files (dict) files = mapFiles(directory) # validate working directory structure and contents (no output) validateDirectories(directory, verbose=args['verbose']) # communicate with user