def get_contigs(self, token=None, ref=None, contig_id_list=None):
assembly_api = AssemblyAPI(self.services, token, ref)
if contig_id_list is None:
result = assembly_api.get_contigs()
else:
result = assembly_api.get_contigs(contig_id_list)
return {x: ttypes.AssemblyContig(**result[x]) for x in result}
def get_contig_gc_content(self, token=None, ref=None, contig_id_list=None):
assembly_api = AssemblyAPI(self.services, token, ref)
if contig_id_list is None:
result = assembly_api.get_contig_gc_content()
else:
result = assembly_api.get_contig_gc_content(contig_id_list)
return result
def setup():
shared.setup()
global t_new, t_old, t_new_e, t_old_e, t_client_new, t_client_old, g_skip_shock
g_skip_shock = not shared.services["shock_service_url"].startswith("http")
t_new = AssemblyAPI(shared.services, shared.token, assembly_new)
t_new_e = _Assembly(shared.services, shared.token, assembly_new)
t_old = AssemblyAPI(shared.services, shared.token, assembly_old)
t_old_e = _KBaseGenomes_ContigSet(shared.services, shared.token,
assembly_old)
t_client_new = AssemblyClientAPI(shared.services["assembly_service_url"],
shared.token, assembly_new)
t_client_old = AssemblyClientAPI(shared.services["assembly_service_url"],
shared.token, assembly_old)
count = 0
limit = 10000
skip = 0
done = False
while not done:
results = ws.list_objects({"workspaces": [fix_workspace],
"type": "KBaseGenomeAnnotations.Assembly",
"skip": skip,
"limit": limit})
if len(results) == 0:
done = True
for x in results:
count += 1
ac = AssemblyAPI(services, token, ref="{}/{}".format(fix_workspace, x[1]))
handle_ref = ac.get_data()["fasta_handle_ref"]
shock_node_id = None
try:
handle = hc.hids_to_handles([handle_ref])[0]
shock_node_id = handle["id"]
except Exception, e:
print "Failed to retrieve handle {} from {}".format(handle_ref,
services["handle_service_url"])
_log.exception(e)
shock_node_id = handle_ref
print "#"*80
print x[1], shock_node_id
print "#"*80
def get_number_contigs(self, token=None, ref=None):
assembly_api = AssemblyAPI(self.services, token, ref)
result = assembly_api.get_number_contigs()
return result
def get_stats(self, token=None, ref=None):
assembly_api = AssemblyAPI(self.services, token, ref)
result = assembly_api.get_stats()
return ttypes.AssemblyStats(**result)
def get_external_source_info(self, token=None, ref=None):
assembly_api = AssemblyAPI(self.services, token, ref)
result = assembly_api.get_external_source_info()
return ttypes.AssemblyExternalSourceInfo(**result)
def get_genome_annotations(self, token=None, ref=None):
assembly_api = AssemblyAPI(self.services, token, ref)
result = assembly_api.get_genome_annotations(ref_only=True)
return result
def get_assembly_id(self, token=None, ref=None):
assembly_api = AssemblyAPI(self.services, token, ref)
result = assembly_api.get_assembly_id()
return result
done = False
while not done:
results = ws.list_objects({
"workspaces": [fix_workspace],
"type": "KBaseGenomeAnnotations.Assembly",
"skip": skip,
"limit": limit
})
if len(results) == 0:
done = True
for x in results:
count += 1
ac = AssemblyAPI(services,
token,
ref="{}/{}".format(fix_workspace, x[1]))
handle_ref = ac.get_data()["fasta_handle_ref"]
shock_node_id = None
try:
handle = hc.hids_to_handles([handle_ref])[0]
shock_node_id = handle["id"]
except Exception, e:
print "Failed to retrieve handle {} from {}".format(
handle_ref, services["handle_service_url"])
_log.exception(e)
shock_node_id = handle_ref
print "#" * 80
print x[1], shock_node_id
#!/usr/bin/python
#Usage: python data_api_test.py ws-url shock-url handle-url token ref id
import sys
import json
import doekbase.data_api
from doekbase.data_api.sequence.assembly.api import AssemblyAPI , AssemblyClientAPI
assemb = AssemblyAPI({
'workspace_service_url' : sys.argv[1],
'shock_service_url' : sys.argv[2],
'handle_service_url' : sys.argv[3]
},token = sys.argv[4],ref = sys.argv[5]);
contigset = {
'id' : sys.argv[6],
'name' : assemb.get_external_source_info()["external_source_id"],
'md5' : "",
'source_id' : assemb.get_external_source_info()["external_source_id"],
'source' : assemb.get_external_source_info()["external_source"],
'type' : "Genome",
'contigs' : []
};
contigdata = assemb.get_contigs();
for contigid in contigdata.keys():
newcontig = {
'id' : contigdata[contigid]['contig_id'],
'length' : contigdata[contigid]['length'],
'md5' : contigdata[contigid]['md5'],
