def __init__(self, wbuildConfig):
"""
Parse wbuild/snakemake config object for DROP-specific content
:param wbuildConfig: wBuild config object
"""
self.wBuildConfig = wbuildConfig
self.config_dict = self.setDefaults(wbuildConfig.getConfig())
self.root = Path(self.get("root"))
self.processedDataDir = self.root / "processed_data"
self.processedResultsDir = self.root / "processed_results"
utils.createDir(self.root)
utils.createDir(self.processedDataDir)
utils.createDir(self.processedResultsDir)
self.htmlOutputPath = Path(self.get("htmlOutputPath"))
self.readmePath = Path(self.get("readmePath"))
# annotations
self.geneAnnotation = self.get("geneAnnotation")
self.genomeAssembly = self.get("genomeAssembly")
self.fastaFile = self.get("mae")[
"genome"] # TODO: move fasta outside of mae
self.fastaDict = Path(self.fastaFile).with_suffix(".dict")
self.sampleAnnotation = SampleAnnotation(self.get("sampleAnnotation"),
self.root)
# submodules
self.AE = AE(config=self.get("aberrantExpression"),
sampleAnnotation=self.sampleAnnotation,
processedDataDir=self.processedDataDir,
processedResultsDir=self.processedResultsDir)
self.AS = AS(config=self.get("aberrantSplicing"),
sampleAnnotation=self.sampleAnnotation,
processedDataDir=self.processedDataDir,
processedResultsDir=self.processedResultsDir)
self.MAE = MAE(config=self.get("mae"),
sampleAnnotation=self.sampleAnnotation,
processedDataDir=self.processedDataDir,
processedResultsDir=self.processedResultsDir)
# counts export
self.exportCounts = ExportCounts(
dict_=self.get("exportCounts"),
outputRoot=self.processedResultsDir,
sampleAnnotation=self.sampleAnnotation,
geneAnnotations=self.getGeneAnnotations(),
genomeAssembly=self.get("genomeAssembly"),
aberrantExpression=self.AE,
aberrantSplicing=self.AS)
# legacy
utils.setKey(self.config_dict, None, "aberrantExpression",
self.AE.dict_)
utils.setKey(self.config_dict, None, "aberrantSplicing", self.AS.dict_)
utils.setKey(self.config_dict, None, "mae", self.MAE.dict_)
def __init__(self, wbuildConfig):
"""
Parse wbuild/snakemake config object for DROP-specific content
:param wbuildConfig: wBuild config object
"""
self.wBuildConfig = wbuildConfig
self.config_dict = self.setDefaults(wbuildConfig.getConfig())
self.root = Path(self.get("root"))
self.processedDataDir = self.root / "processed_data"
self.processedResultsDir = self.root / "processed_results"
utils.createDir(self.root)
utils.createDir(self.processedDataDir)
utils.createDir(self.processedResultsDir)
self.htmlOutputPath = Path(self.get("htmlOutputPath"))
self.readmePath = Path(self.get("readmePath"))
self.geneAnnotation = self.get("geneAnnotation")
self.genomeAssembly = self.get("genomeAssembly")
self.sampleAnnotation = SampleAnnotation(self.get("sampleAnnotation"),
self.root)
# setup submodules
cfg = self.config_dict
sa = self.sampleAnnotation
pd = self.processedDataDir
pr = self.processedResultsDir
self.AE = AE(cfg["aberrantExpression"], sa, pd, pr)
self.AS = AS(cfg["aberrantSplicing"], sa, pd, pr)
self.MAE = MAE(cfg["mae"], sa, pd, pr)
self.exportCounts = ExportCounts(self.config_dict,
self.processedResultsDir,
self.sampleAnnotation,
self.getGeneAnnotations(),
self.get("genomeAssembly"),
aberrantExpression=self.AE,
aberrantSplicing=self.AS)
# legacy
utils.setKey(self.config_dict, None, "aberrantExpression",
self.AE.dict_)
utils.setKey(self.config_dict, None, "aberrantSplicing", self.AS.dict_)
utils.setKey(self.config_dict, None, "mae", self.MAE.dict_)
def __init__(self, wbuildConfig, workDir):
"""
Parse wbuild/snakemake config object for DROP-specific content
:param wbuildConfig: wBuild config object
:param workDir: path to project working directory
"""
self.workDir = Path(workDir)
self.wBuildConfig = wbuildConfig
self.config_dict = self.setDefaults(wbuildConfig.getConfig())
self.root = Path(self.get("root"))
self.processedDataDir = self.root / "processed_data"
self.processedResultsDir = self.root / "processed_results"
utils.createDir(self.root)
utils.createDir(self.processedDataDir)
utils.createDir(self.processedResultsDir)
self.htmlOutputPath = Path(self.get("htmlOutputPath"))
self.readmePath = Path(self.get("readmePath"))
# annotations
self.genome = Genome(
annotation=self.get("geneAnnotation"),
assembly=self.get("genomeAssembly"),
reference=self.get("genome")
)
self.sampleAnnotation = SampleAnnotation(
file=self.get("sampleAnnotation"),
root=self.root,
genome=self.genome
)
# submodules
self.AE = AE(
config=self.get("aberrantExpression"),
sampleAnnotation=self.sampleAnnotation,
processedDataDir=self.processedDataDir,
processedResultsDir=self.processedResultsDir,
workDir=workDir
)
self.AS = AS(
config=self.get("aberrantSplicing"),
sampleAnnotation=self.sampleAnnotation,
processedDataDir=self.processedDataDir,
processedResultsDir=self.processedResultsDir,
workDir=workDir
)
self.MAE = MAE(
config=self.get("mae"),
sampleAnnotation=self.sampleAnnotation,
processedDataDir=self.processedDataDir,
processedResultsDir=self.processedResultsDir,
workDir=workDir,
genome=self.genome
)
# counts export
self.exportCounts = ExportCounts(
dict_=self.get("exportCounts"),
outputRoot=self.processedResultsDir,
sampleAnnotation=self.sampleAnnotation,
genome=self.genome,
aberrantExpression=self.AE,
aberrantSplicing=self.AS
)
# write sample params for each module AS not currently supported
sampleParams = SampleParams(
self.AE,
self.AS,
self.MAE,
self.get("geneAnnotation"),
self.processedDataDir,
self.sampleAnnotation
)
# legacy
utils.setKey(self.config_dict, None, "aberrantExpression", self.AE.dict_)
utils.setKey(self.config_dict, None, "aberrantSplicing", self.AS.dict_)
utils.setKey(self.config_dict, None, "mae", self.MAE.dict_)