def main():
######################
# Parse command line #
######################
args = argumentsParser()
##########
# Logger #
##########
common.parametersLogger(args)
#############
# Constants #
#############
common.global_dict['dataDirectory'] = '.'
boxName = common.global_dict['boxName']['GetINSDCFiles']
common.global_dict.setdefault('files', {}).setdefault(
boxName,
{}).setdefault('inputClusteringStep',
'{}_correspondences.tsv'.format(args.OutputName))
common.global_dict.setdefault('files', {}).setdefault(
boxName,
{}).setdefault('report',
'{}_{}_report.txt'.format(args.OutputName, boxName))
#######
# Run #
#######
run(args.UniProtACList)
def main():
######################
# Parse command line #
######################
args, parser = argumentsParser()
for key, value in {
'Identity': args.Identity,
'Coverage': args.Coverage
}.items():
if not (0 < value <= 1):
parser.error(
'ValueError: value of --{} option must be a float number according to the condition: 0 < value <= 1'
.format(key))
##########
# Logger #
##########
common.parametersLogger(args)
#########################
# Dependancies checking #
#########################
common.dependenciesChecking()
#############
# Constants #
#############
common.global_dict['dataDirectory'] = '.'
boxName = common.global_dict['boxName']['ClusteringIntoFamilies']
common.global_dict.setdefault('files', {}).setdefault(
boxName,
{}).setdefault('proteins_2',
'{}_proteins_familiesStep.json'.format(args.outputName))
common.global_dict.setdefault('files', {}).setdefault(
boxName, {}).setdefault(
'families', '{}_families.tsv'.format(
os.path.join(common.global_dict['dataDirectory'], boxName,
args.outputName)))
common.global_dict.setdefault('files', {}).setdefault(
boxName,
{}).setdefault('report',
'{}_{}_report.txt'.format(args.outputName, boxName))
#######
# Run #
#######
run(args.FastaFile, args.inputProteins, args.Identity, args.Coverage,
args.MMseqsAdvancedSettings)
def main():
######################
# Parse command line #
######################
args = argumentsParser()
##########
# Logger #
##########
common.parametersLogger(args)
#############
# Constants #
#############
common.global_dict['dataDirectory'] = '.'
boxName = common.global_dict['boxName']['SyntenyFinder']
common.global_dict.setdefault('files',
{}).setdefault(boxName, {}).setdefault(
'nodes',
'{}_nodes.json'.format(args.outputName))
common.global_dict.setdefault('files',
{}).setdefault(boxName, {}).setdefault(
'edges',
'{}_edges.json'.format(args.outputName))
common.global_dict.setdefault('files', {}).setdefault(
boxName,
{}).setdefault('proteins',
'{}_proteins_syntenyStep.json'.format(args.outputName))
common.global_dict.setdefault('files', {}).setdefault(
boxName,
{}).setdefault('report',
'{}_{}_report.txt'.format(args.outputName, boxName))
#######
# Run #
#######
run(args.inputProteins, args.inputTargets, args.WindowSize,
args.SyntenyGap, args.SyntenyScoreCutoff,
args.ClusteringAdvancedSettings)
def main():
######################
# Parse command line #
######################
args = argumentsParser()
##########
# Logger #
##########
common.parametersLogger(args)
#########################
# Dependancies checking #
#########################
common.dependenciesChecking()
#############
# Constants #
#############
common.global_dict['dataDirectory'] = '.'
boxName = common.global_dict['boxName']['ParseINSDCFiles_GetTaxonomy']
common.global_dict.setdefault('files', {}).setdefault(boxName, {}).setdefault(
'faa', '{}.faa'.format(os.path.join(common.global_dict['dataDirectory'], boxName, args.outputName)))
common.global_dict.setdefault('files', {}).setdefault(boxName, {}).setdefault(
'organisms_1', '{}_organisms_parsingStep.json'.format(os.path.join(common.global_dict['dataDirectory'], boxName, args.outputName)))
common.global_dict.setdefault('files', {}).setdefault(boxName, {}).setdefault(
'organisms_2', '{}_organisms_taxonomyStep.json'.format(args.outputName))
common.global_dict.setdefault('files', {}).setdefault(boxName, {}).setdefault(
'proteins_1', '{}_proteins_parsingStep.json'.format(os.path.join(common.global_dict['dataDirectory'], boxName, args.outputName)))
common.global_dict.setdefault('files', {}).setdefault(boxName, {}).setdefault(
'targets_1', '{}_targets_parsingStep.json'.format(os.path.join(common.global_dict['dataDirectory'], boxName, args.outputName)))
common.global_dict.setdefault('files', {}).setdefault(boxName, {}).setdefault(
'targets_2', '{}_targets_taxonomyStep.json'.format(args.outputName))
common.global_dict.setdefault('files', {}).setdefault(boxName, {}).setdefault(
'report', '{}_{}_report.txt'.format(args.outputName, boxName))
#######
# Run #
#######
run(args.CorrespondencesFile, args.IncludedPseudogenes)
def main():
######################
# Parse command line #
######################
args = argumentsParser()
##########
# Logger #
##########
common.parametersLogger(args)
logger = logging.getLogger('main')
#########################
# Dependancies checking #
#########################
common.dependenciesChecking()
##############
# Constantes #
##############
args.OutputDirName = args.OutputDirName.strip('/')
common.constantsInitialization(args.OutputDirName, args.UniProtACList,
args.CorrespondencesFile)
ORDERBOX = orderDefinition(args.UniProtACList, args.CorrespondencesFile)
logger.debug('ORDERBOX: {}'.format(ORDERBOX))
############
# Switches #
############
if args.newProject and os.path.isdir(
common.global_dict['workingDirectory']):
shutil.rmtree(common.global_dict['workingDirectory'])
checkSameVersion(common.global_dict['versionFileName'])
if not os.path.isfile(common.global_dict['settingsFileName']):
if os.path.isdir(common.global_dict['workingDirectory']):
logger.error(
'{} already existing directory and not dedicated to NetSyn project. Please change your project name or use --newProject option'
.format(common.global_dict['workingDirectory']))
logger.error(
'Project name already used. Please change your project name or use --newProject.'
)
exit(1)
'''Pas de dernier setting == premiere analyse'''
logger.info('New NetSyn project: {}'.format(
common.global_dict['workingDirectory']))
os.mkdir(common.global_dict['workingDirectory'])
os.mkdir(common.global_dict['dataDirectory'])
analysisNumber, resultsDirectory = getAnalysisNumber(
args.OutputDirName)
common.filesNameInitialization(resultsDirectory, args.OutputDirName,
analysisNumber)
try:
saveInputFiles(args.UniProtACList, args.CorrespondencesFile)
except:
shutil.rmtree(common.global_dict['workingDirectory'])
exit(1)
runFromBox = ORDERBOX[0]
nameBoxToResum = None
nameBoxDone = None
else:
'''Fichier de setting == analyse deja lance'''
nameBoxToResum = getBoxToResum(args)
if nameBoxToResum == 'General informations':
logger.error(
'Already existing project. Please start a new project')
exit(1)
else:
inputFilesModificationChecking(args.UniProtACList,
args.CorrespondencesFile)
logger.info('NetSyn project recovery: {}'.format(
common.global_dict['workingDirectory']))
nameBoxDone = getLastBoxDone(ORDERBOX)
runFromBox = resumptionFrom(nameBoxToResum, nameBoxDone, ORDERBOX)
analysisNumber, resultsDirectory = getAnalysisNumber(
args.OutputDirName)
common.filesNameInitialization(resultsDirectory, args.OutputDirName,
analysisNumber)
createYamlSettingsFile(args, ORDERBOX)
if runFromBox:
'''Execution a partir de la boite x'''
runFromBoxIndex = ORDERBOX.index(runFromBox)
updateLastBoxDone(ORDERBOX[runFromBoxIndex -
1] if runFromBoxIndex - 1 >= 0 else '')
logger.debug('Box from which resume: {}'.format(nameBoxToResum))
logger.debug('Last box done: {}'.format(nameBoxDone))
logger.debug('Run from: {}'.format(runFromBox))
writeCurrentVersion(common.global_dict['version'],
common.global_dict['versionFileName'])
boxesManager(runFromBox, resultsDirectory, analysisNumber, ORDERBOX,
args)
else:
'''Nous avons deja des resultats'''
logger.debug('Box from which resume: {}'.format(nameBoxToResum))
logger.debug('Last box done: {}'.format(nameBoxDone))
logger.debug('Run from: {}'.format(runFromBox))
logger.info('This analysis already exists')