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