def get_kegg_modules(expand_nested_modules=True):
results = list()
for line in pv(list(kegg_list("module")), "Parsing module files"):
line = line.strip()
module, name = line.split("\t")
prefix, id_module = module.split(":")
module_file = kegg_get(module)
module_info = parse_kegg_module(module_file)
results.append(module_info)
df = pd.DataFrame(results)
df.index.name = datetime.datetime.now().strftime(
"Accessed: %Y-%m-%d @ %H:%M [{}]".format(time.tzname[0]))
# Expand nested modules
if expand_nested_modules:
for id_module, row in df.iterrows():
kegg_orthology_set = row["ORTHOLOGY_SET"]
expanded = set()
for x in kegg_orthology_set:
if x.startswith("K"):
expanded.add(x)
if x.startswith("M"):
for id_ko in df.loc[x, "ORTHOLOGY_SET"]:
expanded.add(id_ko)
df.loc[id_module, "ORTHOLOGY_SET"] = expanded
return df
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 getNodeNames(type):
list = kegg_list(type).read()
names = dict()
entries = list.split('\n')
for entry in entries[:len(entries) - 1]:
e = entry.split('\t')
nodeId = e[0][4:]
lastIndex = e[1].find(';')
name = e[1][:lastIndex] if lastIndex >= 0 else e[1]
if type == "hsa":
lastIndex = name.find(',')
name = name[:lastIndex] if lastIndex >= 0 else name
names[nodeId] = name
return names
def get_node_names(type):
list = kegg_list(type).read()
names = dict()
entries = list.split('\n')
for entry in entries[:len(entries) - 1]:
e = entry.split('\t')
node_id = e[0][4:]
last_index = e[1].find(';')
name = e[1][:last_index] if last_index >= 0 else e[1]
if type == "hsa":
last_index = name.find(',')
name = name[:last_index] if last_index >= 0 else name
names[node_id] = name
return names
def test_list_pathway(self):
with kegg_list("pathway") as handle:
handle.read()
self.assertEqual(handle.url, "http://rest.kegg.jp/list/pathway")
def list_pathways():
res = kegg_list('pathway', 'hsa').read()
return res
parser.add_argument('--clear', action='store_true', help='clear the graph')
parser.add_argument('--commitEvery', type=int, default=100, help='commit every x steps')
args = parser.parse_args()
importer = GraphImporter(args.db, args.commitEvery)
if args.clear or True:
importer.delete_all()
if not os.path.exists(args.data_dir):
os.makedirs(args.data_dir)
files = [f for f in listdir(args.data_dir) if isfile(join(args.data_dir, f))]
if len(files) == 0:
# download kgml files
res = kegg_list('pathway', 'hsa').read()
items = res.split('\n')
for item in items[:len(items) - 1]:
pathway_id = item[5:13]
if pathway_id != 'hsa01100':
print('fetching ' + pathway_id)
kgml = kegg_get(pathway_id, 'kgml').read()
with open(args.data_dir + pathway_id + '.kgml', 'w') as text_file:
text_file.write(kgml)
files = [f for f in listdir(args.data_dir) if isfile(join(args.data_dir, f))]
def getNodeNames(type):
list = kegg_list(type).read()
names = dict()
def parse_kegg(org_id, strain, sourcedb, session):
# get pathways for organism specified by org_id
pathways = kegg_list(database='pathway', org=org_id).read().split('path:')
path_ids = []
# make list of path ids to iterate through
for path in pathways:
if path != '':
path_ids.append(path[:8])
# iterate through each path and obtain interactions
for path in path_ids:
# get kgml representation of path
kgml_path = read(kegg_get(path, option='kgml'))
path_name = kgml_path._getname()
# dictionary of compounds in current path (node_id: kegg_id)
# compound._getid() returns node id (only relevant in context of current path)
# compound._getname() returns kegg id (relevant in overall KEGG DB)
compound_ids = {}
for compound in kgml_path.compounds:
compound_ids[compound._getid()] = compound._getname()[-6:]
# go through each relation in path
for relation in kgml_path.relations:
relation_type = relation.element.attrib['type']
# ignore maplink relations
if relation_type == 'maplink': continue
# relation._getentry1/2() returns protein id (locus) or compound id (KEGG id)
entries = [relation._getentry1()._getname(), relation._getentry2()._getname()]
# if one or both interactors are listed as undefined, move on to next interaction
if (entries[0] == 'undefined') | (entries[1] == 'undefined'): continue
# list to hold existing interactors
interactors = [[], []]
# list to hold new metabolite ids for interactions with metabolites not yet in the database
new_metabolites = [[], []]
# go through each entry in the relation
for num in range(0, 2):
# each entry may contain >1 id; go through all of them
for id in entries[num].split(' '):
if id == '': continue
# if interactor is not protein or compound, continue
if (id.split(':')[0] != org_id) & (id.split(':')[1] not in kegg_compounds): continue
# check if the id is a kegg id by searching in kegg_compounds
kegg_id= None
if id.split(':')[1] in kegg_compounds:
kegg_id = id.split(':')[1]
# check if interactor (protein) already exists
if (kegg_id is None) & (org_id != 'eco'):
interactor = session.query(Interactor).get(id.split(':')[1])
if interactor is not None:
# make sure to add None value; this will be needed to create interaction reference later
# None is appended rather than the interactor id because the interactor is not an ortholog
interactors[num].append([interactor, None])
# if it doesnt exist, it's not a valid protein, so check if it is a valid compound
elif kegg_id is not None:
interactor = session.query(Metabolite).filter_by(kegg = kegg_id).first()
# if metabolite with id was not found, append the kegg_id to new_metabolites to create
if interactor is None:
new_metabolites[num].append(kegg_id)
else:
# if the metabolite was found, add it to the existing interactor list
interactors[num].append([interactor, interactor.id])
# if parsing E. coli path, add all orthologs to interactor list
elif org_id == 'eco':
for ortholog in session.query(OrthologEcoli).filter_by(ortholog_id = id.split(':')[1],
strain_protein = strain).all():
if ortholog is not None:
# add the id of the ecoli protein for the interaction reference later
interactors[num].append([ortholog.protein, id.split(':')[1]])
# create list of interactor pairs from two separate lists
interactor_pairs = []
# create interactor pairs from interactors which already exist in db
for interactor1 in interactors[0]:
for interactor2 in interactors[1]:
if (interactor1[0].type != 'm') | (interactor2[0].type != 'm'):
interactor_pairs.append([interactor1, interactor2])
# create interactor pair from interactors and new metabolites
for interactor1 in interactors[0]:
for id in new_metabolites[1]:
# ignore interactor pairs which would result in m-m interactions
if interactor1[0].type == 'm': continue
# Note: can query metabolite with kegg only because we updated the metabolite info first
metabolite = session.query(Metabolite).filter_by(kegg = id).first()
if metabolite is None:
metabolite = Metabolite(id = id, kegg = id, pubchem = kegg_compounds[id]['pubchem'],
chebi = kegg_compounds[id]['chebi'])
session.add(metabolite)
interactor_pairs.append([interactor1, [metabolite, metabolite.id]])
for interactor1 in interactors[1]:
for id in new_metabolites[0]:
if interactor1[0].type == 'm': continue
metabolite = session.query(Metabolite).filter_by(kegg = id).first()
if metabolite is None:
metabolite = Metabolite(id = id, kegg = id, pubchem = kegg_compounds[id]['pubchem'],
chebi = kegg_compounds[id]['chebi'])
session.add(metabolite)
interactor_pairs.append([interactor1, [metabolite, metabolite.id]])
# if no interactor pairs were found, move on the the next interaction
if len(interactor_pairs) == 0: continue
# get all intermediates in reaction of type compound
intermeds = []
for subtype in relation.element.iter(tag='subtype'):
# if the subtype element is a compound, get its node id
if 'compound' in subtype.attrib:
compound_node_id = subtype.attrib['compound']
if compound_node_id is None: continue
# if the node id was not stored in the compound ids for this path, move on to the next sybtype
if int(compound_node_id) not in compound_ids: continue
# if compound id is valid, either add existing matching metabolite or create new one and add
kegg_id = compound_ids[int(compound_node_id)]
metabolite = session.query(Metabolite).filter_by(kegg = kegg_id).first()
if metabolite is None:
metabolite = Metabolite(id=kegg_id, name=kegg_compounds[kegg_id]['name'],
pubchem=kegg_compounds[kegg_id]['pubchem'],
chebi=kegg_compounds[kegg_id]['chebi'], kegg=kegg_id)
session.add(metabolite)
intermeds.append([metabolite, metabolite.id])
# add protein - intermediate interactor pairs
for interactor_list in interactors:
for interactor in interactor_list:
if interactor[0].type != 'm':
for intermed in intermeds:
interactor_pairs.append([interactor, intermed])
# go through each interaction pair and add interaction if it doesnt exist yet
for interactor_pair in interactor_pairs:
homogenous = (interactor_pair[0][0] == interactor_pair[1][0])
interaction = session.query(Interaction).filter(Interaction.interactors.contains(interactor_pair[0][0]),
Interaction.interactors.contains(interactor_pair[1][0]),
Interaction.homogenous == homogenous).first()
source = session.query(InteractionSource).filter_by(data_source=sourcedb).first()
#create interaction if it doesnt exist yet, add source to its sources if it isn't already
if interaction is None:
interaction = Interaction(type=interactor_pair[0][0].type + '-' + interactor_pair[1][0].type,
strain=strain, homogenous=homogenous,
interactors=[interactor_pair[0][0], interactor_pair[1][0]])
interaction.sources.append(source)
if org_id == 'eco':
interaction.ortholog_derived = 'Ecoli'
session.add(interaction), session.commit()
elif source not in interaction.sources:
interaction.sources.append(source)
# in case the interaction already existed, make sure interactor_a and interactor_b variables for
# new interaction reference match up with the first and second interactors of the existing
# interaction (so it's easy to see which Pseudomonas interactor matches up with which Ecoli
# ortholog if the org id is eco)
interactor_a, interactor_b = None, None
if org_id == 'eco':
if interaction.interactors[0] == interactor_pair[0][0]:
interactor_a = interactor_pair[0][1]
interactor_b = interactor_pair[1][1]
else:
interactor_b = interactor_pair[0][1]
interactor_a = interactor_pair[1][1]
# search for reference
reference = session.query(InteractionReference).filter_by(source_db='kegg',
comment='in ' + path_name + ' path',
interactor_a=interactor_a,
interactor_b=interactor_b).first()
# if the reference doesnt exist, create it, add it to the interaction's references and add the source
# to the reference's sources
if reference is None:
reference = InteractionReference(source_db='kegg', comment='in ' + path_name + ' path',
interactor_a=interactor_a, interactor_b=interactor_b)
interaction.references.append(reference)
reference.sources.append(source)
# if the reference does exist, add it to the interaction's reference list and add the source to the
# reference's source list if it isn't there already
else:
if interaction not in reference.interactions:
reference.interactions.append(interaction)
if source not in reference.sources:
reference.sources.append(source)
session.commit()
print(sourcedb, session.query(Interaction).count())
def test_list_cpd_C01290_list_gl_G0009(self):
with kegg_list(["cpd:C01290", "gl:G00092"]) as handle:
handle.read()
self.assertEqual(handle.url,
"http://rest.kegg.jp/list/cpd:C01290+gl:G00092")
def test_list_T01001(self):
with kegg_list("T01001") as handle:
handle.read()
self.assertEqual(handle.url, "http://rest.kegg.jp/list/T01001")
def test_list_T01001(self):
h = kegg_list("T01001")
h.read()
self.assertEqual(h.url, "http://rest.kegg.jp/list/T01001")
h.close()
def test_list_hsa(self):
h = kegg_list("hsa")
h.read()
self.assertEqual(h.url, "http://rest.kegg.jp/list/hsa")
h.close()
def test_list_organism(self):
h = kegg_list("organism")
h.read()
self.assertEqual(h.url, "http://rest.kegg.jp/list/organism")
h.close()
def test_list_pathway(self):
h = kegg_list("pathway")
h.read()
self.assertEqual(h.url, "http://rest.kegg.jp/list/pathway")
h.close()
from Bio.KEGG.REST import kegg_list, kegg_get
from Bio.KEGG.KGML import KGML_parser
from import_utils import add_edge, add_node
datapath = os.path.dirname(os.path.realpath(__file__)) + "/data/"
if not os.path.exists(datapath):
os.makedirs(datapath)
files = [f for f in listdir(datapath) if isfile(join(datapath, f))]
if len(files) == 0:
# download kgml files
res = kegg_list('pathway', 'hsa').read()
items = res.split("\n")
for item in items[:len(items) - 1]:
pathway_id = item[5:13]
print("fetching " + pathway_id)
kgml = kegg_get(pathway_id, "kgml").read()
with open(datapath + pathway_id + ".kgml", "w") as text_file:
text_file.write(kgml)
files = [f for f in listdir(datapath) if isfile(join(datapath, f))]
def get_names(names):
n = names.replace("...", "", -14)
return n.split(", ")
def test_list_organism(self):
with kegg_list("organism") as handle:
handle.read()
self.assertEqual(handle.url, "http://rest.kegg.jp/list/organism")
def test_list_hsa(self):
with kegg_list("hsa") as handle:
handle.read()
self.assertEqual(handle.url, "http://rest.kegg.jp/list/hsa")
def test_list_hsa_10458_list_ece_Z5100(self):
h = kegg_list(["hsa:10458", "ece:Z5100"])
h.read()
self.assertEqual(h.url, "http://rest.kegg.jp/list/hsa:10458+ece:Z5100")
h.close()
def test_list_hsa_10458_list_ece_Z5100(self):
with kegg_list(["hsa:10458", "ece:Z5100"]) as handle:
handle.read()
self.assertEqual(handle.url,
"http://rest.kegg.jp/list/hsa:10458+ece:Z5100")
def test_list_cpd_C01290_list_gl_G0009(self):
h = kegg_list(["cpd:C01290", "gl:G00092"])
h.read()
self.assertEqual(h.url,
"http://rest.kegg.jp/list/cpd:C01290+gl:G00092")
h.close()
def test_list_C01290_list_G00092(self):
with kegg_list(["C01290", "G00092"]) as handle:
handle.read()
self.assertEqual(handle.url, "http://rest.kegg.jp/list/C01290+G00092")
def test_list_C01290_plus_G00092(self):
h = kegg_list("C01290+G00092")
h.read()
self.assertEqual(h.url, "http://rest.kegg.jp/list/C01290+G00092")
h.close()