def gwas_run_gwas2(meth, genotype=None, kinship_matrix=None, traits=None, out=None):
"""Computes association between each SNP and a trait of interest that has been scored
across a large number of individuals. This method takes Filtered SNP object,
kinship matrix, trait object as input and computes association.
:param genotype: Population variation object
:type genotype: kbtypes.KBaseGwasData.GwasPopulationVariation
:param kinship_matrix: Kinship matrix object id
:type kinship_matrix: kbtypes.KBaseGwasData.GwasPopulationKinship
:param traits: Trait object id
:type traits: kbtypes.KBaseGwasData.GwasPopulationTrait
:param out: Output
:type out: kbtypes.KBaseGwasData.GwasTopVariations
: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, "variation_id" : genotype, "trait_id" : traits, "kinship_id": kinship_matrix, "out_id" : out, "comment" : "comment"}
meth.advance("submit job to run GWAS analysis")
try:
jid = gc.run_gwas(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="GWAS analysis using emma", running="GWAS analysis using emma").run(jid[0])
return _workspace_output(out)
def gwas_run_gwas2(meth,
genotype=None,
kinship_matrix=None,
traits=None,
out=None):
"""Computes association between each SNP and a trait of interest that has been scored
across a large number of individuals. This method takes Filtered SNP object,
kinship matrix, trait object as input and computes association.
:param genotype: Population variation object
:type genotype: kbtypes.KBaseGwasData.GwasPopulationVariation
:param kinship_matrix: Kinship matrix object id
:type kinship_matrix: kbtypes.KBaseGwasData.GwasPopulationKinship
:param traits: Trait object id
:type traits: kbtypes.KBaseGwasData.GwasPopulationTrait
:param out: Output
:type out: kbtypes.KBaseGwasData.GwasTopVariations
: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,
"variation_id": genotype,
"trait_id": traits,
"kinship_id": kinship_matrix,
"out_id": out,
"comment": "comment"
}
meth.advance("submit job to run GWAS analysis")
try:
jid = gc.run_gwas(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="GWAS analysis using emma",
running="GWAS analysis using emma").run(jid[0])
return _workspace_output(out)
