def test_KeggParser():
s = KeggParser()
d = s.parse(s.get("cpd:C00001"))
d = s.parse(s.get("ds:H00001"))
d = s.parse(s.get("dr:D00001"))
d = s.parse(s.get("ev:E00001"))
d = s.parse(s.get("ec:1.1.1.1"))
d = s.parse(s.get("hsa:1525"))
d = s.parse(s.get("genome:T00001"))
d = s.parse(s.get("gl:G00001"))
d = s.parse(s.get("md:hsa_M00554"))
d = s.parse(s.get("ko:K00001"))
d = s.parse(s.get("path:hsa04914"))
d = s.parse(s.get("rc:RC00001"))
d = s.parse(s.get("rn:R00001"))
d = s.parse(s.get("rp:RP00001"))
def __init__(self, verbosity="INFO"):
super(Mapper, self).__init__(level=verbosity)
self.logging.info("Initialising the services")
self.logging.info("... uniprots")
self._uniprot_service = UniProt()
self.logging.info("... KEGG")
self._kegg_service = KeggParser(verbose=False)
self.logging.info("... HGNC")
self._hgnc_service = HGNC()
self.logging.info("... UniChem")
self._unichem_service = UniChem()
self.logging.info("...BioDBNet")
self._biodbnet = BioDBNet()
def __init__(self, verbose=True):
self._kegg_service = KeggParser(verbose=verbose)
print("Loading all gene identifiers for HSA")
names = self._kegg_service.list("hsa")
names = names.strip().split("\n")
names = [x.split("\t")[0] for x in names]
self._names = names[:]
print("Fetching all data")
self.alldata = {}
self.load_all_kegg_entries()
print("Building the dataframe")
try:
self.df = self.build_dataframe()
except:
print("error in build_dataframe")
try:
entries = [
"hsa:" + x['entry'].split()[0] for x in self.mcresults if x
]
for entry, result in zip(entries, self.mcresults):
self.alldata[entry] = result
except:
print("something wrng happened while scaning mcresults")
#import pickle
#pickle.dump(results, open("kegg_gene.dat","w"))
from bioservices import KeggParser
kegg = KeggParser(verbose=False)
def test_func(names):
from easydev import MultiProcessing
t = MultiProcessing(verbose=False, maxcpu=8)
for name in names:
t.add_job(keggfunc, name)
t.run()
return t
def keggfunc(name):
global kegg
try:
id_ = kegg.get(name)
