def setDefaults(self, config_dict):
"""
Check mandatory keys and set defaults for any missing keys
:param config_dict: config dictionary
:return: config dictionary with defaults
"""
# check mandatory keys
config_dict = utils.checkKeys(
config_dict,
keys=["htmlOutputPath", "root", "sampleAnnotation"],
check_files=True)
config_dict["geneAnnotation"] = utils.checkKeys(
config_dict["geneAnnotation"], keys=None, check_files=True)
config_dict["wBuildPath"] = utils.getWBuildPath()
setKey = utils.setKey
setKey(config_dict, None, "fileRegex", ".*\.(R|md)")
setKey(config_dict, None, "genomeAssembly", "hg19")
# set submodule dictionaries
setKey(config_dict, None, "aberrantExpression", dict())
setKey(config_dict, None, "aberrantSplicing", dict())
setKey(config_dict, None, "mae", dict())
setKey(config_dict, None, "exportCounts", dict())
# commandline tools
setKey(config_dict, None, "tools", dict())
setKey(config_dict, ["tools"], "samtoolsCmd", "samtools")
setKey(config_dict, ["tools"], "bcftoolsCmd", "bcftools")
setKey(config_dict, ["tools"], "gatkCmd", "gatk")
return config_dict
def setDefaults(self, config_dict):
"""
Check mandatory keys and set defaults for any missing keys
:param config_dict: config dictionary
:return: config dictionary with defaults
"""
# check mandatory keys
config_dict = utils.checkKeys(
config_dict,
keys=["htmlOutputPath", "root", "sampleAnnotation"],
check_files=True)
config_dict["geneAnnotation"] = utils.checkKeys(
config_dict["geneAnnotation"], keys=None, check_files=True)
config_dict["wBuildPath"] = utils.getWBuildPath()
setKey = utils.setKey
setKey(config_dict, None, "fileRegex", r".*\.(R|md)")
setKey(config_dict, None, "genomeAssembly", "hg19")
hpo_url = 'https://www.cmm.in.tum.de/public/paper/drop_analysis/resource/hpo_genes.tsv.gz'
setKey(config_dict, None, "hpoFile", hpo_url)
# set submodule dictionaries
setKey(config_dict, None, "aberrantExpression", dict())
setKey(config_dict, None, "aberrantSplicing", dict())
setKey(config_dict, None, "mae", dict())
setKey(config_dict, None, "rnaVariantCalling", dict())
setKey(config_dict, None, "exportCounts", dict())
# Legacy check: If mae still defines genome print warning, otherwise use the
# globally defined genome
try:
genome_files = self.get("mae")["genome"]
logger.info(
"WARNING: Using the mae defined genome instead of the globally defined one.\n"
"This will be deprecated in the future to allow for reference genomes to"
" be defined in the sample annotation table. Please update your config "
"and sample annotation table\n")
except KeyError:
genome_files = self.get("genome")
setKey(config_dict, None, "genome", genome_files)
# commandline tools
setKey(config_dict, None, "tools", dict())
setKey(config_dict, ["tools"], "samtoolsCmd", "samtools")
setKey(config_dict, ["tools"], "bcftoolsCmd", "bcftools")
setKey(config_dict, ["tools"], "gatkCmd", "gatk")
return config_dict
def setDefaultKeys(self, dict_):
super().setDefaultKeys(dict_)
setKey = utils.setKey
dict_ = utils.checkKeys(dict_, keys=["repeat_mask"], check_files=True)
groups = setKey(dict_, None, "groups", self.sa.getGroups(assay="RVC"))
setKey(dict_, None, "knownVCFs", [])
setKey(dict_, None, "repeat_mask", "")
setKey(dict_, None, "hcArgs", "")
setKey(dict_, None, "minAlt", 3)
return dict_
def setDefaultKeys(self, dict_):
super().setDefaultKeys(dict_)
setKey = utils.setKey
dict_ = utils.checkKeys(dict_, keys=["qcVcf"], check_files=True)
groups = setKey(dict_, None, "groups", self.sa.getGroups(assay="DNA"))
setKey(dict_, None, "qcGroups", groups)
setKey(dict_, None, "gatkIgnoreHeaderCheck", True)
setKey(dict_, None, "padjCutoff", .05)
setKey(dict_, None, "allelicRatioCutoff", 0.8)
setKey(dict_, None, "maxAF", .001)
setKey(dict_, None, "gnomAD", False)
return dict_