def maf(meth, maf=0.05, variation=None, out=None, comment=None):
"""Perform filtering on Minor allele frequency (MAF).
Minor allele frequency (MAF) refers to the frequency at which the least common
<a href="http://en.wikipedia.org/wiki/Allele">allele</a> occurs in a given population.
:param maf: Minor allele frequency
:type maf: kbtypes.Numeric
:param variation: Population variation object
:type variation: kbtypes.KBaseGwasData.GwasPopulationVariation
:param out: Population variation, filtered
:type out: kbtypes.KBaseGwasData.GwasPopulationVariation
:param comment: Comment
:type comment: kbtypes.Unicode
:return: Workspace ID of filtered data
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
meth.stages = 3
meth.advance("init GWAS service")
gc = GWAS(URLS.gwas, token=meth.token)
argsx = {"ws_id" : meth.workspace_id, "inobj_id" : variation, "outobj_id" : out, "minor_allele_frequency" : maf, "comment" : "comment"}
meth.advance("submit job to filter VCF")
try:
jid = gc.prepare_variation(argsx)
except Exception as err:
raise GWASException("submit job failed: {}".format(err))
if not jid:
raise GWASException(2, "submit job failed, no job id")
AweJob.URL = URLS.awe
AweJob(meth, started="run VCF", running="VCF").run(jid[0])
return _workspace_output(out)
def maf(meth, maf=0.05, variation=None, out=None, comment=None):
"""Perform filtering on Minor allele frequency (MAF).
Minor allele frequency (MAF) refers to the frequency at which the least common
<a href="http://en.wikipedia.org/wiki/Allele">allele</a> occurs in a given population.
:param maf: Minor allele frequency
:type maf: kbtypes.Numeric
:param variation: Population variation object
:type variation: kbtypes.KBaseGwasData.GwasPopulationVariation
:param out: Population variation, filtered
:type out: kbtypes.KBaseGwasData.GwasPopulationVariation
:param comment: Comment
:type comment: kbtypes.Unicode
:return: Workspace ID of filtered data
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
meth.stages = 3
meth.advance("init GWAS service")
gc = GWAS(URLS.gwas, token=meth.token)
argsx = {
"ws_id": meth.workspace_id,
"inobj_id": variation,
"outobj_id": out,
"minor_allele_frequency": maf,
"comment": "comment"
}
meth.advance("submit job to filter VCF")
try:
jid = gc.prepare_variation(argsx)
except Exception as err:
raise GWASException("submit job failed: {}".format(err))
if not jid:
raise GWASException(2, "submit job failed, no job id")
AweJob.URL = URLS.awe
AweJob(meth, started="run VCF", running="VCF").run(jid[0])
return _workspace_output(out)
