def importRepeatsFromUCSC(outfile):
"""This task downloads UCSC repeats types as identified
in the configuration file.
"""
gtfsubset.getRepeatDataFromUCSC(dbhandle=connectToUCSC(),
repclasses=P.as_list(
PARAMS["ucsc_repeattypes"]),
outfile=outfile,
job_memory=PARAMS["job_memory"])
def importRNAAnnotationFromUCSC(outfile):
"""This task downloads UCSC repetetive RNA types.
"""
gtfsubset.getRepeatDataFromUCSC(
dbhandle=connectToUCSC(),
repclasses=P.as_list(PARAMS["ucsc_rnatypes"]),
outfile=outfile,
remove_contigs_regex=PARAMS["ncbi_remove_contigs"],
job_memory=PARAMS["job_memory"])