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expt_config_parser.py
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expt_config_parser.py
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from configparser import ConfigParser
import os
import fnmatch
# Parse and validate the input of an experiment config file
# output a dict with all of the parameters needed to process experiments
def parseExptConfig(configFile, librariesToSublibrariesDict):
parser = ConfigParser()
results = parser.read(configFile)
if len(results) == 0:
return None, 1, 'Experiment config file not found'
# output variables
paramDict = dict()
exitStatus = 0
warningString = ''
# check all sections
expectedSections = set(['experiment_settings',
'library_settings',
'counts_files',
'filter_settings',
'sgrna_analysis',
'growth_values',
'gene_analysis'])
parsedSections = set(parser.sections())
if len(expectedSections) != len(parsedSections) and len(expectedSections) != len(expectedSections.intersection(parsedSections)):
return paramDict, 1, 'Config file does not have all required sections or has extraneous sections!\nExpected:' + ','.join(expectedSections) + '\nFound:' + ','.join(parsedSections)
# experiment settings
if parser.has_option('experiment_settings', 'output_folder'):
# ways to check this is a valid path?
paramDict['output_folder'] = parser.get(
'experiment_settings', 'output_folder')
else:
warningString += 'No output folder specified, defaulting to current directory\n.'
paramDict['output_folder'] = os.curdir()
if parser.has_option('experiment_settings', 'experiment_name'):
paramDict['experiment_name'] = parser.get(
'experiment_settings', 'experiment_name')
else:
warningString += 'No experiment name specified, defaulting to \'placeholder_expt_name\'\n.'
paramDict['experiment_name'] = 'placeholder_expt_name'
# library settings
libraryDict = librariesToSublibrariesDict
if parser.has_option('library_settings', 'library'):
parsedLibrary = parser.get('library_settings', 'library')
if parsedLibrary.lower() in libraryDict:
paramDict['library'] = parsedLibrary.lower()
else:
warningString += 'Library name \"%s\" not recognized\n' % parsedLibrary
exitStatus += 1
else:
warningString += 'No library specified\n'
exitStatus += 1
parsedLibrary = ''
if 'library' in paramDict:
if parser.has_option('library_settings', 'sublibraries'):
parsedSubList = parser.get(
'library_settings', 'sublibraries').strip().split('\n')
paramDict['sublibraries'] = []
for sub in parsedSubList:
sub = sub.lower()
if sub in libraryDict[paramDict['library']]:
paramDict['sublibraries'].append(sub)
else:
warningString += 'Sublibrary %s not recognized\n' % sub
else:
paramDict['sublibraries'] = libraryDict[paramDict['library']]
# counts files
if parser.has_option('counts_files', 'counts_file_string'):
countsFileString = parser.get(
'counts_files', 'counts_file_string').strip()
paramDict['counts_file_list'] = []
for stringLine in countsFileString.split('\n'):
stringLine = stringLine.strip()
if len(stringLine.split(':')) != 2 or len(stringLine.split('|')) != 2:
warningString += 'counts file entry could not be parsed: ' + stringLine + '\n'
exitStatus += 1
else:
parsedPath = stringLine.split(':')[0]
if os.path.isfile(parsedPath) == False:
warningString += 'Counts file not found: ' + parsedPath + '\n'
exitStatus += 1
condition, replicate = stringLine.split(':')[1].split('|')
paramDict['counts_file_list'].append(
(condition, replicate, parsedPath))
else:
warningString += 'No counts files entered\n'
exitStatus += 1
# filter settings
filterOptions = ['either', 'both']
if parser.has_option('filter_settings', 'filter_type') and parser.get('filter_settings', 'filter_type').lower() in filterOptions:
paramDict['filter_type'] = parser.get(
'filter_settings', 'filter_type').lower()
else:
warningString += 'Filter type not set or not recognized, defaulting to \'either\'\n'
paramDict['filter_type'] = 'either'
if parser.has_option('filter_settings', 'minimum_reads'):
try:
paramDict['minimum_reads'] = parser.getint(
'filter_settings', 'minimum_reads')
except ValueError:
# recommended value is 50 but seems arbitrary to default to that
warningString += 'Minimum read value not an integer, defaulting to 0\n'
paramDict['minimum_reads'] = 0
else:
# recommended value is 50 but seems arbitrary to default to that
warningString += 'Minimum read value not found, defaulting to 0\n'
paramDict['minimum_reads'] = 0
# sgRNA Analysis
if parser.has_option('sgrna_analysis', 'condition_string'):
conditionString = parser.get(
'sgrna_analysis', 'condition_string').strip()
paramDict['condition_tuples'] = []
if 'counts_file_list' in paramDict:
expectedConditions = set(
list(zip(*paramDict['counts_file_list']))[0])
else:
expectedConditions = []
enteredConditions = set()
for conditionStringLine in conditionString.split('\n'):
conditionStringLine = conditionStringLine.strip()
if len(conditionStringLine.split(':')) != 3:
warningString += 'Phenotype condition line not understood: ' + \
conditionStringLine + '\n'
exitStatus += 1
else:
phenotype, condition1, condition2 = conditionStringLine.split(
':')
if condition1 not in expectedConditions or condition2 not in expectedConditions:
warningString += 'One of the conditions entered does not correspond to a counts file: ' + \
conditionStringLine + '\n'
exitStatus += 1
else:
paramDict['condition_tuples'].append(
(phenotype, condition1, condition2))
enteredConditions.add(condition1)
enteredConditions.add(condition2)
if len(paramDict['condition_tuples']) == 0:
warningString += 'No phenotype score/condition pairs found\n'
exitStatus += 1
unusedConditions = list(expectedConditions - enteredConditions)
if len(unusedConditions) > 0:
warningString += 'Some conditions assigned to counts files will not be incorporated in sgRNA analysis:\n' \
+ ','.join(unusedConditions) + '\n'
else:
warningString += 'No phenotype score/condition pairs entered\n'
exitStatus += 1
pseudocountOptions = ['zeros only', 'all values', 'filter out']
if parser.has_option('sgrna_analysis', 'pseudocount_behavior') and parser.get('sgrna_analysis', 'pseudocount_behavior').lower() in pseudocountOptions:
paramDict['pseudocount_behavior'] = parser.get(
'sgrna_analysis', 'pseudocount_behavior').lower()
else:
warningString += 'Pseudocount behavior not set or not recognized, defaulting to \'zeros only\'\n'
paramDict['pseudocount_behavior'] = 'zeros only'
if parser.has_option('sgrna_analysis', 'pseudocount'):
try:
paramDict['pseudocount'] = parser.getfloat(
'sgrna_analysis', 'pseudocount')
except ValueError:
warningString += 'Pseudocount value not an number, defaulting to 0.1\n'
paramDict['pseudocount'] = 0.1
else:
warningString += 'Pseudocount value not found, defaulting to 0.1\n'
paramDict['pseudocount'] = 0.1
# Growth Values
if parser.has_option('growth_values', 'growth_value_string') and len(parser.get('growth_values', 'growth_value_string').strip()) != 0:
growthValueString = parser.get(
'growth_values', 'growth_value_string').strip()
if 'condition_tuples' in paramDict and 'counts_file_list' in paramDict:
expectedComparisons = set(
list(zip(*paramDict['condition_tuples']))[0])
expectedReplicates = set(
list(zip(*paramDict['counts_file_list']))[1])
expectedTupleList = []
for comp in expectedComparisons:
for rep in expectedReplicates:
expectedTupleList.append((comp, rep))
else:
expectedTupleList = []
enteredTupleList = []
growthValueTuples = []
for growthValueLine in growthValueString.split('\n'):
growthValueLine = growthValueLine.strip()
linesplit = growthValueLine.split(':')
if len(linesplit) != 3:
warningString += 'Growth value line not understood: ' + growthValueLine + '\n'
exitStatus += 1
continue
comparison = linesplit[0]
replicate = linesplit[1]
try:
growthVal = float(linesplit[2])
except ValueError:
warningString += 'Growth value not a number: ' + growthValueLine + '\n'
exitStatus += 1
continue
curTup = (comparison, replicate)
if curTup in expectedTupleList:
if curTup not in enteredTupleList:
enteredTupleList.append(curTup)
growthValueTuples.append(
(comparison, replicate, growthVal))
else:
warningString += ':'.join(curTup) + \
' has multiple growth values entered\n'
exitStatus += 1
else:
warningString += ':'.join(
curTup) + ' was not expected given the specified counts file assignments and sgRNA phenotypes\n'
exitStatus += 1
# because we enforced no duplicates or unexpected values these should match up unless there were values not entered
# require all growth values to be explictly entered if some were
if len(enteredTupleList) != len(expectedTupleList):
warningString += 'Growth values were not entered for all expected comparisons/replicates. Expected: ' + \
','.join([':'.join(tup) for tup in expectedTupleList]) + '\nEntered: ' + \
','.join([':'.join(tup) for tup in enteredTupleList]) + '\n'
exitStatus += 1
else:
paramDict['growth_value_tuples'] = growthValueTuples
else:
warningString += 'No growth values--all phenotypes will be reported as log2enrichments\n'
paramDict['growth_value_tuples'] = []
if 'condition_tuples' in paramDict and 'counts_file_list' in paramDict:
expectedComparisons = set(
list(zip(*paramDict['condition_tuples']))[0])
expectedReplicates = set(
list(zip(*paramDict['counts_file_list']))[1])
for comp in expectedComparisons:
for rep in expectedReplicates:
paramDict['growth_value_tuples'].append((comp, rep, 1))
# Gene Analysis
if parser.has_option('gene_analysis', 'collapse_to_transcripts'):
try:
paramDict['collapse_to_transcripts'] = parser.getboolean(
'gene_analysis', 'collapse_to_transcripts')
except ValueError:
warningString += 'Collapse to transcripts entry not a recognized boolean value\n'
exitStatus += 1
else:
paramDict['collapse_to_transcripts'] = True
warningString += 'Collapse to transcripts defaulting to True\n'
# pseudogene parameters
if parser.has_option('gene_analysis', 'generate_pseudogene_dist'):
paramDict['generate_pseudogene_dist'] = parser.get(
'gene_analysis', 'generate_pseudogene_dist').lower()
if paramDict['generate_pseudogene_dist'] not in ['auto', 'manual', 'off']:
warningString += 'Generate pseudogene dist entry not a recognized option\n'
exitStatus += 1
else:
paramDict['generate_pseudogene_dist'] = False
warningString += 'Generate pseudogene dist defaulting to False\n'
if 'generate_pseudogene_dist' in paramDict and paramDict['generate_pseudogene_dist'] == 'manual':
if parser.has_option('gene_analysis', 'pseudogene_size'):
try:
paramDict['pseudogene_size'] = parser.getint(
'gene_analysis', 'pseudogene_size')
except ValueError:
warningString += 'Pseudogene size entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No pseudogene size provided\n'
exitStatus += 1
if parser.has_option('gene_analysis', 'num_pseudogenes'):
try:
paramDict['num_pseudogenes'] = parser.getint(
'gene_analysis', 'num_pseudogenes')
except ValueError:
warningString += 'Pseudogene number entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No pseudogene size provided\n'
# list possible analyses in param dict as dictionary with keys = analysis and values = analysis-specific params
paramDict['analyses'] = dict()
# analyze by average of best n
if parser.has_option('gene_analysis', 'calculate_ave'):
try:
if parser.getboolean('gene_analysis', 'calculate_ave') == True:
paramDict['analyses']['calculate_ave'] = []
except ValueError:
warningString += 'Calculate ave entry not a recognized boolean value\n'
exitStatus += 1
if 'calculate_ave' in paramDict['analyses']:
if parser.has_option('gene_analysis', 'best_n'):
try:
paramDict['analyses']['calculate_ave'].append(
parser.getint('gene_analysis', 'best_n'))
except ValueError:
warningString += 'Best_n entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No best_n value provided for average analysis function\n'
exitStatus += 1
else:
warningString += 'Best n average analysis not specified, defaulting to False\n'
# analyze by Mann-Whitney
if parser.has_option('gene_analysis', 'calculate_mw'):
try:
if parser.getboolean('gene_analysis', 'calculate_mw') == True:
paramDict['analyses']['calculate_mw'] = []
except ValueError:
warningString += 'Calculate Mann-Whitney entry not a recognized boolean value\n'
exitStatus += 1
# analyze by K-S, skipping for now
# analyze by nth best sgRNA
if parser.has_option('gene_analysis', 'calculate_nth'):
try:
if parser.getboolean('gene_analysis', 'calculate_nth') == True:
paramDict['analyses']['calculate_nth'] = []
except ValueError:
warningString += 'Calculate best Nth sgRNA entry not a recognized boolean value\n'
exitStatus += 1
if 'calculate_nth' in paramDict['analyses']:
if parser.has_option('gene_analysis', 'nth'):
try:
paramDict['analyses']['calculate_nth'].append(
parser.getint('gene_analysis', 'nth'))
except ValueError:
warningString += 'Nth best sgRNA entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No Nth best value provided for that analysis function\n'
exitStatus += 1
else:
warningString += 'Nth best sgRNA analysis not specified, defaulting to False\n'
if len(paramDict['analyses']) == 0:
# should this raise exitStatus?
warningString += 'No analyses selected to compute gene scores\n'
return paramDict, exitStatus, warningString
# Parse the library configuration file to get the available libraries, sublibraries, and corresponding library table files
def parseLibraryConfig(libConfigFile):
parser = ConfigParser()
result = parser.read(libConfigFile)
if len(result) == 0:
raise ValueError('Library config file not found')
librariesToSublibraries = dict()
librariesToTables = dict()
for library in parser.sections():
tableFile = parser.get(library, 'filename').strip()
librariesToTables[library.lower()] = tableFile
sublibraryList = parser.get(
library, 'sublibraries').strip().split('\n')
librariesToSublibraries[library.lower()] = [sub.strip().lower()
for sub in sublibraryList]
if len(librariesToTables) == 0:
raise ValueError('Library config file empty')
return librariesToSublibraries, librariesToTables