def gwas_run_kinship(meth, filtered_variation=None, out=None, comment=None):
"""Computes the n by n kinship matrix for a set of n related subjects.
The kinship matrix defines pairwise genetic relatedness among individuals and
is estimated by using all genotyped markers. This requires the filtered SNPs as input.
:param filtered_variation: Population variation, filtered
:type filtered_variation: kbtypes.KBaseGwasData.GwasPopulationVariation
:param out: Computed Kinship matrix
:type out: kbtypes.KBaseGwasData.GwasPopulationKinship
:param comment: Comment
:type comment: kbtypes.Unicode
:return: New workspace object
: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" : filtered_variation, "outobj_id" : out, "comment" : "comment"}
meth.advance("submit job to select_random_snps")
try:
jid = gc.calculate_kinship_matrix(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="Calculate Kinship matrix", running="Kinship matrix").run(jid[0])
return _workspace_output(out)
def gwas_run_kinship(meth, filtered_variation=None, out=None, comment=None):
"""Computes the n by n kinship matrix for a set of n related subjects.
The kinship matrix defines pairwise genetic relatedness among individuals and
is estimated by using all genotyped markers. This requires the filtered SNPs as input.
:param filtered_variation: Population variation, filtered
:type filtered_variation: kbtypes.KBaseGwasData.GwasPopulationVariation
:param out: Computed Kinship matrix
:type out: kbtypes.KBaseGwasData.GwasPopulationKinship
:param comment: Comment
:type comment: kbtypes.Unicode
:return: New workspace object
: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": filtered_variation,
"outobj_id": out,
"comment": "comment"
}
meth.advance("submit job to select_random_snps")
try:
jid = gc.calculate_kinship_matrix(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="Calculate Kinship matrix",
running="Kinship matrix").run(jid[0])
return _workspace_output(out)
