def get_kegg_compounds():
# fill in compounds dictionary (kegg_id: {name: '', pubchem: '', chebi: ''})
for compound in kegg_list(database='compound'):
kegg_compounds[compound[4:10]] = {}
kegg_compounds[compound[4:10]]['name'] = compound.split('\t')[1].split(';')[0].rstrip()
kegg_compounds[compound[4:10]]['chebi'] = None
kegg_compounds[compound[4:10]]['pubchem'] = None
# had to change kegg_conv source code to accept 'chebi' as target db for kegg_conv
for cpd_id in kegg_conv('chebi', 'compound').read().split('cpd:'):
if cpd_id != '':
kegg_compounds[cpd_id[:6]]['chebi'] = cpd_id.split('chebi:')[1].rstrip()
for cpd_id in kegg_conv('pubchem', 'compound').read().split('cpd:'):
if cpd_id != '':
kegg_compounds[cpd_id[:6]]['pubchem'] = cpd_id.split('pubchem:')[1].rstrip()
def test_conv_ncbi_gi_hsa_10458_list_ece_Z5100(self):
with kegg_conv("ncbi-gi", ["hsa:10458", "ece:Z5100"]) as handle:
handle.read()
self.assertEqual(
handle.url, "http://rest.kegg.jp/conv/ncbi-gi/hsa:10458+ece:Z5100")
def test_conv_ncbi_geneid_eco(self):
with kegg_conv("ncbi-geneid", "eco") as handle:
handle.read()
self.assertEqual(handle.url,
"http://rest.kegg.jp/conv/ncbi-geneid/eco")
def test_conv_ncbi_gi_hsa_10458_list_ece_Z5100(self):
h = kegg_conv("ncbi-gi", ["hsa:10458", "ece:Z5100"])
h.read()
self.assertEqual(
h.url, "http://rest.kegg.jp/conv/ncbi-gi/hsa:10458+ece:Z5100")
h.close()
def test_conv_ncbi_geneid_eco(self):
h = kegg_conv("ncbi-geneid", "eco")
h.read()
self.assertEqual(h.url, "http://rest.kegg.jp/conv/ncbi-geneid/eco")
h.close()
