def gene_network2ws(meth, feature_set_id=None, out_id=None):
""" Query all available network data in KBase central store.
:param feature_set_id: FeatureSet workspace object id
:type feature_set_id: kbtypes.KBaseSearch.FeatureSet
:param out_id: Output Networks object identifier
:type out_id: kbtypes.KBaseNetworks.Network
: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)
meth.advance("Retrieve genes from workspace")
ws = Workspace2(token=meth.token, wsid=meth.workspace_id)
fs = ws.get(feature_set_id)
qid2cds = ids2cds(fs['elements'].keys())
gl_str = ",".join(list(set(qid2cds.values())));
meth.advance("Running GeneList to Networks")
argsx = {"ws_id" : meth.workspace_id, "inobj_id" : gl_str, "outobj_id": out_id}
try:
gl_oid = gc.genelist_to_networks(argsx)
except Exception as err:
raise GWASException("submit job failed: {}".format(err))
meth.advance("Returning object")
return _workspace_output(out_id)
def gene_network2ws(meth, obj_id=None, out_id=None):
"""This method displays a gene list
along with functional annotation in a table.
:param obj_id: Gene List workspace object identifier.
:type obj_id: kbtypes.KBaseGwasData.GwasGeneList
:param out_id: Output Networks object identifier
:type out_id: kbtypes.KBaseNetworks.Network
:return: New workspace object
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
# :param workspace_id: Workspace name (if empty, defaults to current workspace)
# :type workspace_id: kbtypes.Unicode
meth.stages = 3
meth.advance("init GWAS service")
gc = GWAS(URLS.gwas, token=meth.token)
meth.advance("Retrieve genes from workspace")
# if not workspace_id:
# meth.debug("Workspace ID is empty, setting to current ({})".format(meth.workspace_id))
# workspace_id = meth.workspace_id
ws = Workspace2(token=meth.token, wsid=meth.workspace_id)
raw_data = ws.get(obj_id)
gl = [gr[2] for gr in raw_data['genes']]
gl_str = ",".join(gl)
meth.advance("Running GeneList to Networks")
argsx = {
"ws_id": meth.workspace_id,
"inobj_id": gl_str,
"outobj_id": out_id
}
try:
gl_oid = gc.genelist_to_networks(argsx)
except Exception as err:
raise GWASException("submit job failed: {}".format(err))
#if not gl_oid: # it may return empty string based on current script
# raise GWASException(2, "submit job failed, no job id")
meth.advance("Returning object")
return _workspace_output(out_id)
def gene_network2ws(meth, obj_id=None, out_id=None):
"""This method displays a gene list
along with functional annotation in a table.
:param obj_id: Gene List workspace object identifier.
:type obj_id: kbtypes.KBaseGwasData.GwasGeneList
:param out_id: Output Networks object identifier
:type out_id: kbtypes.KBaseNetworks.Network
:return: New workspace object
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
# :param workspace_id: Workspace name (if empty, defaults to current workspace)
# :type workspace_id: kbtypes.Unicode
meth.stages = 3
meth.advance("init GWAS service")
gc = GWAS(URLS.gwas, token=meth.token)
meth.advance("Retrieve genes from workspace")
# if not workspace_id:
# meth.debug("Workspace ID is empty, setting to current ({})".format(meth.workspace_id))
# workspace_id = meth.workspace_id
ws = Workspace2(token=meth.token, wsid=meth.workspace_id)
raw_data = ws.get(obj_id)
gl = [ gr[2] for gr in raw_data['genes']]
gl_str = ",".join(gl);
meth.advance("Running GeneList to Networks")
argsx = {"ws_id" : meth.workspace_id, "inobj_id" : gl_str, "outobj_id": out_id}
try:
gl_oid = gc.genelist_to_networks(argsx)
except Exception as err:
raise GWASException("submit job failed: {}".format(err))
#if not gl_oid: # it may return empty string based on current script
# raise GWASException(2, "submit job failed, no job id")
meth.advance("Returning object")
return _workspace_output(out_id)
def gene_network2ws(meth, feature_set_id=None, out_id=None):
""" Query all available network data in KBase central store.
:param feature_set_id: FeatureSet workspace object id
:type feature_set_id: kbtypes.KBaseSearch.FeatureSet
:param out_id: Output Networks object identifier
:type out_id: kbtypes.KBaseNetworks.Network
: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)
meth.advance("Retrieve genes from workspace")
ws = Workspace2(token=meth.token, wsid=meth.workspace_id)
fs = ws.get(feature_set_id)
qid2cds = ids2cds(fs['elements'].keys())
gl_str = ",".join(list(set(qid2cds.values())))
meth.advance("Running GeneList to Networks")
argsx = {
"ws_id": meth.workspace_id,
"inobj_id": gl_str,
"outobj_id": out_id
}
try:
gl_oid = gc.genelist_to_networks(argsx)
except Exception as err:
raise GWASException("submit job failed: {}".format(err))
meth.advance("Returning object")
return _workspace_output(out_id)
