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}
'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'],
'sequence' : contigdata[contigid]['sequence'],
'genetic_code' : sys.argv[7],
'replicon_type' : "linear",
'replicon_geometry' : "linear",
'name' : contigdata[contigid]['contig_id'],
'description' : contigdata[contigid]['description'],
'complete' : 1
};
if contigdata[contigid]['is_circular'] == 1:
newcontig['replicon_type'] = "circular";
