def subsetWells(df_mapping_dict, criteria, hypothesis, verbose=False):
'''
Tag wells that meet user-passed criteria.
Args:
df (pandas.DataFrame) must have Plate_IDs and Well as columns
criteria (dictionary) with mapping variables (str) as keys and accepted instances (str) as values
hypothesis (dictionary)
verbose (boolean)
Returns:
df (pandas.DataFrame)
'''
if (len(criteria) == 0):
smartPrint('No subsetting was requested.\n', verbose)
return df_mapping_dict, None
for plate_id, mapping_df in df_mapping_dict.items():
# subsetting on number-based criteria does not match hits due to type mismatch (str vs int/float)
mapping_df_str = mapping_df.astype(str)
remove_boolean = ~(mapping_df_str.isin(criteria).sum(1)
== len(criteria)).values # list of booleans
remove_idx = mapping_df_str.index[remove_boolean]
mapping_df.loc[remove_idx, 'Subset'] = [0] * len(remove_idx)
msg = 'The following criteria were used to subset data:\n'
msg += tidyDictPrint(criteria)
smartPrint(msg, verbose)
return df_mapping_dict, msg
def flagWells(df, flags, verbose=False, drop=False):
'''
Passes plate-well-specific flags from user into mapping dataframes.
Args:
df (dictionary of pandas.DataFrame) must have Plate_IDs and Well as columns
flags (dictionary) with Plate_IDs (str) as keys and Wells (stR) as vlaues
verbose (boolean)
Returns:
df (pandas.DataFrame)
'''
if (len(flags) == 0):
smartPrint('No wells were flagged.\n', verbose)
return df
for plate, wells in flags.items():
if plate in df.keys():
df[plate].loc[wells, 'Flag'] = [1] * len(wells)
if drop: df[plate] = df[plate][df[plate].Flag == 0]
smartPrint('The following flags were detected:\n', verbose)
smartPrint(tidyDictPrint(flags), verbose)
return df
def print_arguments(args):
msg = '\n'
msg += tidyMessage('User provided the following command-line arguments:')
msg += '\n'
msg += tidyDictPrint(vars(args))
print(msg)
def print_defaults(self):
parser = argparse.ArgumentParser(
description=
'Print in terminal default values stored in libs/config.py')
msg = '\nDefault settings for select variables. '
msg += 'You can adjust these values in "amiga/libs/config.py". \n\n'
msg += tidyDictPrint(config)
sys.exit(msg)
def parseCommand():
'''
Interprets the arguments passed by the user to AMiGA.
Note: Function is AMiGA-specific and should not be used verbatim for other apps.
Returns:
args (dict): a dictionary with keys as suggested variable names
and keys as the user-passed and argparse-interpreted arguments.
'''
args_dict = {}
# parse arguments
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input', required=True)
parser.add_argument('-o', '--output', required=True)
parser.add_argument('-s', '--subset', required=False)
parser.add_argument('-v', '--value', required=True)
parser.add_argument('-x', '--x-variable', required=True)
parser.add_argument('-y', '--y-variable', required=True)
parser.add_argument('-p', '--operation', required=False)
parser.add_argument('-f', '--filter', required=False)
parser.add_argument('-t', '--title', required=False)
parser.add_argument('--kwargs', required=False)
parser.add_argument('--verbose', action='store_true', default=False)
# pass arguments to local variables
args = parser.parse_args()
args_dict['fi'] = args.input # File path provided by user
args_dict['fo'] = args.output
args_dict['s'] = args.subset
args_dict['x'] = args.x_variable
args_dict['y'] = args.y_variable
args_dict['v'] = args.value
args_dict['p'] = args.operation
args_dict['f'] = args.filter
args_dict['t'] = args.title
args_dict['kwargs'] = args.kwargs
args_dict['verbose'] = args.verbose
# summarize command-line artguments and print
if args_dict['verbose']:
msg = '\n'
msg += tidyMessage(
'User provided the following command-line arguments:')
msg += '\n'
msg += tidyDictPrint(args_dict)
print(msg)
return args_dict
def interpretParameters(files, args, verbose=False):
'''
Checks specific directories for their existence and makes sure data was
provided by user. It will also compose and can print a message that can
communicate with user the results of this validation.
Args:
files (dict): keys are parameter names and values are file paths
args (dict): keys are parameter names and values are corresponding command-line arguments
Returns:
params_dict (dict): dictionary where keys are variables and values instances
'''
# params_settings defines parameters for interpreting parameter files or argument calls
#
# each item is a 3-tuple where:
# 1. parameter name which matches both input argument and text file name (str)
# 2. delimitor that separates values of a variable of the parameter (str)
# 3. integerize: whether to convert values of a variable to integers (boolean)
params_settings = [('interval', ',', True), ('subset', ',', False),
('flag', ',', False), ('hypo', '\+|,', False)]
# initialize all parameters based on their settings
params_dict = {}
for pp, sep, integerize in params_settings:
params_dict[pp] = initializeParameter(files[pp],
args[pp],
sep=sep,
integerize=integerize)
smartPrint(tidyDictPrint(params_dict), verbose)
# if user requests any subsetting, summary results must be merged
if params_dict['subset']:
args['merges'] = True
msg = 'WARNING: Because user has requested subsetting of data, '
msg += 'results will be merged into single summary and/or data file.\n'
smartPrint(msg, verbose)
return params_dict, args
def parseCommand(config):
'''
Interprets the arguments passed by the user to AMiGA. If the verobse argument
is set to True, argumentParser will also print a message summarizing the
the user-passed command-line arguments.
Note: Function is AMiGA-specific and should not be used verbatim for other apps.
Args:
config (dictionary): variables saved in config.py where key is variable and value is value
Returns:
args (dict): a dictionary with keys as suggested variable names
and keys as the user-passed and argparse-interpreted arguments.
'''
args_dict = {}
# parse arguments
parser = argparse.ArgumentParser()
# defining input/output
parser.add_argument('-i', '--input', required=True)
parser.add_argument('-o', '--output', required=False)
# reducing data
parser.add_argument('-f', '--flag', required=False)
parser.add_argument('-s', '--subset', required=False)
# selecting time points
parser.add_argument('-tss',
'--time-step-size',
action='store',
type=int,
default=1) #11
parser.add_argument('-sfn',
'--skip-first-n',
action='store',
type=int,
default=0)
parser.add_argument('-t', '--interval', required=False)
# hypothesis testing
parser.add_argument('-y', '--hypothesis', required=False)
parser.add_argument('-fdr',
'--false-discovery-rate',
action='store',
type=int,
default=10)
parser.add_argument('-np',
'--number-permutations',
action='store',
type=int,
default=0)
parser.add_argument('--subtract-control',
action='store_true',
default=False)
# pooling and normalizations
parser.add_argument('--normalize-parameters',
action='store_true',
default=False)
parser.add_argument('--pool-by', required=False)
parser.add_argument('--normalize-by', required=False)
# plotting
parser.add_argument('--plot', action='store_true', default=False)
parser.add_argument('--plot-derivative',
action='store_true',
default=False)
parser.add_argument('--plot-delta-od', action='store_true', default=True)
parser.add_argument('--dont-plot', action='store_true', default=False)
## saving tables
parser.add_argument('--save-cleaned-data',
action='store_true',
default=False)
parser.add_argument('--save-gp-data', action='store_true', default=False)
parser.add_argument('--save-mapping-tables',
action='store_true',
default=False)
parser.add_argument('--merge-summary', action='store_true', default=False)
## model preferences
parser.add_argument('--fix-noise', action='store_true', default=False)
parser.add_argument('--sample-posterior',
action='store_true',
default=False)
parser.add_argument('--include-gaussian-noise',
action='store_true',
default=False)
## user communication
parser.add_argument('--only-basic-summary',
action='store_true',
default=False)
parser.add_argument('--only-print-defaults',
action='store_true',
default=False)
parser.add_argument('-v', '--verbose', action='store_true', default=False)
# pass arguments to local variables
args = parser.parse_args()
args_dict['fpath'] = args.input # File path provided by user
args_dict['flag'] = args.flag
args_dict['subset'] = args.subset
args_dict['hypo'] = args.hypothesis
args_dict['interval'] = args.interval
args_dict['plot'] = args.plot
args_dict['verbose'] = args.verbose
args_dict['nperm'] = args.number_permutations
args_dict['nthin'] = args.time_step_size
args_dict['nskip'] = args.skip_first_n
args_dict['fdr'] = args.false_discovery_rate
args_dict['pool'] = [1 if args.pool_by is not None else 0
][0] #: args.pool_replicates
args_dict['merges'] = args.merge_summary
args_dict['norm'] = args.normalize_parameters
args_dict['pd'] = args.plot_derivative
args_dict['pdo'] = args.plot_delta_od
args_dict['obs'] = args.only_basic_summary
args_dict['scd'] = args.save_cleaned_data
args_dict['sgd'] = args.save_gp_data
args_dict['smt'] = args.save_mapping_tables
args_dict['opd'] = args.only_print_defaults
args_dict['sc'] = args.subtract_control
args_dict['dp'] = args.dont_plot
args_dict['fout'] = args.output
args_dict['pb'] = args.pool_by
args_dict['nb'] = args.normalize_by
args_dict['fn'] = args.fix_noise
args_dict['slf'] = args.sample_posterior
args_dict['noise'] = args.include_gaussian_noise
# logical argument definitions
# if normalizing parameters passed,
if args_dict['nb']:
args_dict['norm'] = True
# if subsetting, then merge summary
if args_dict['subset']:
args_dict['merges'] = True
# summarize command-line artguments and print
if args_dict['verbose']:
msg = '\n'
msg += tidyMessage(
'User provided the following command-line arguments:')
msg += '\n'
msg += tidyDictPrint(args_dict)
print(msg)
# print default settings for select variables if prompted by user
if args_dict['opd']:
msg = '\nDefault settings for select variables. '
msg += 'You can adjust these values in amiga/libs/config.py. \n\n'
msg += tidyDictPrint(config)
sys.exit(msg)
# if user requests any subsetting, summary results must be merged
if args_dict['subset'] is not None:
args_dict['merges'] = True
return args_dict