def fidstoextids(fids,retries=0):
if retries > 10: return
idc = IDServerAPI(OTHERURLS.ids)
try:
ext_ids = idc.kbase_ids_to_external_ids(fids)
except:
retries+=1
fidstoextids(fids,retries)
return ext_ids
def writeWS(client, previous_steps):
previous_steps = previous_steps[-1]
#previous_job_id = previous_step["output"].job_id
#pattern = re.compile("\[id=(.*?)]")
#shockid = parselog(previous_job_id,pattern,auth)
#sid = str(shockid).rstrip().split('=')[1].replace(']','')
if 'output' in previous_steps and 'shock_id' in previous_steps['output']:
shock_id = previous_steps['output']['shock_id']
idc = IDServerAPI(OTHERURLS.ids)
name = 'kb|variant.'+str(idc.allocate_id_range(WSTYPES.var_vcftype,1))
obj = { "name": name,
"type": "vcf",
"created":strftime("%d %b %Y %H:%M:%S +0000", gmtime()),
"shock_ref":{ "shock_id" : shock_id,
"shock_url" : OTHERURLS.shock+"/"+shock_id },
"metadata" : meta
}
return ws_saveobject(name,obj, WSTYPES.var_vcftype,meth.workspace_id,meth.token)
def go_anno_net(meth, net_obj_id=None):
"""Add Gene Ontology annotation to network gene nodes
:param net_obj_id: Network object id
:type net_obj_id: kbtypes.KBaseNetworks.Network
:return: Workspace id
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
meth.stages = 5
meth.advance("Prepare annotation service")
#gc = GWAS(URLS.gwas, token=meth.token)
# load from current or other workspace
wsid = meth.workspace_id
# save to current workspace
ws_save_id = meth.workspace_id
meth.advance("Load network object")
wsd = Workspace2(token=meth.token, wsid=wsid)
oc = Ontology(url=URLS.ontology)
net_object = wsd.get(net_obj_id)
nc = Node(net_object['nodes'], net_object['edges'])
idc = IDServerAPI(URLS.ids)
cdmic = CDMI_API(URLS.cdmi)
cdmie = CDMI_EntityAPI(URLS.cdmi)
#idm = IdMap(URLS.idmap)
gids = [
i for i in sorted(nc.ugids.keys()) if 'CDS' in i or 'locus' in i or (
not 'clst' in i and not i.startswith('cluster') and 'ps.' not in i)
]
meth.advance("Get relationships from central data model")
#eids = idc.kbase_ids_to_external_ids(gids)
eids = kb_id2ext_id(idc, gids, 100)
gids2cds = ids2cds(gids)
cgids = gids2cds.values()
cds2l = cds2locus(cgids)
#mrnas_l = cdmie.get_relationship_Encompasses(gids, [], ['to_link'], [])
#mrnas = dict((i[1]['from_link'], i[1]['to_link']) for i in mrnas_l)
#locus_l = cdmie.get_relationship_Encompasses(mrnas.values(), [], ['to_link'], [])
#locus = dict((i[1]['from_link'], i[1]['to_link']) for i in locus_l)
#lgids = [locus[mrnas[i]] for i in gids if i in mrnas.keys()] # ignore original locus ids in gids
lgids = cds2l.values()
meth.advance("Annotate ({:d} nodes, {:d} edges)".format(
len(net_object['nodes']), len(net_object['edges'])))
#ots = oc.get_goidlist(lgids, ['biological_process'], ['IEA'])
ots = oc.get_goidlist(cgids, [], [])
oan = () #oc.get_go_annotation(lgids)
funcs = cdmic.fids_to_functions(lgids)
funcs_org = cdmic.fids_to_functions(cgids)
annotate_nodes(net_object,
ots=ots,
oan=oan,
funcs=funcs,
funcs_org=funcs_org,
eids=eids,
gids2cds=gids2cds,
cds2l=cds2l)
meth.advance("Save annotated object to workspace {}".format(ws_save_id))
obj = {
'type': 'KBaseNetworks.Network',
'data': net_object,
'name': net_obj_id + ".ano",
'meta': {
'original': net_obj_id
}
}
wsd.save_objects({'workspace': ws_save_id, 'objects': [obj]})
return _workspace_output(net_obj_id + ".ano")