def cyview(query,
dataset='HMDB',
connections='targets',
name='',
database=DATABASE):
""" See HMDB/DrugBank graphs with Cytoscape runing on your local machine
`
:param query: Query to select HMDB or DrugBank entries
:param dataset: HMDB or DrugBank, not case sensitive
:param connections: Connection type for DrugBank entries
:param name: Name of the graph on Cytoscape, query is used as default value
:param database: Name of the MongoDB database to connect
"""
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import Style
qc = parseinputquery(query)
print(qc) # todo: tests with HMDB
if dataset.upper() == 'HMDB':
qry = QueryHMDB(index=database)
pairs = qry.getconnectedmetabolites(qc)
mn = qry.get_connections_graph(pairs, query)
else: # assume DrugBank
qry = QueryDrugBank(db, database, 'drugbank')
mn = qry.get_connections_graph(qc, connections)
crcl = CyRestClient()
mn.name = json.dumps(qc) if name == '' else name
cyn = crcl.network.create_from_networkx(mn)
crcl.layout.apply('kamada-kawai', network=cyn)
crcl.style.apply(Style('default'), network=cyn)
def cyview(query):
""" See metabolite networks with Cytoscape runing on your local machine """
from py2cytoscape.data.cyrest_client import CyRestClient
qc = parseinputquery(query)
qry = QueryModelSEED()
mn = qry.get_metabolite_network(qc)
client = CyRestClient()
client.network.create_from_networkx(mn)
def savegraph(query, graphfile, connections='targets'):
"""Save DrugBank interactions as graph files
:param query: MongoDB query clause to select subsets of DrugBank entries
ex: \'{"carriers.name": "Serum albumin"}\'
:param graphfile: File name for saving the output graph
' in GraphML, GML, Cytoscape.js or d3js formats,'
' see readme.md for details'
:param connections: "targets", "enzymes", "transporters" or
"carriers
"""
qry = QueryDrugBank(db, DATABASE, 'drugbank')
qc = parseinputquery(query)
g = qry.get_connections_graph(qc, connections, graphfile)
print(nx.info(g))
def cyview(query, name='', limit=4000):
""" See IntEnz enzyme graphs with Cytoscape runing on your local machine
:param query: Query to select IntEnz entries
:param name: Name of the graph on Cytoscape, query is used as default value
:param limit
"""
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import Style
qc = parseinputquery(query)
qry = QueryIntEnz()
mn = qry.get_connections_graph(qc, limit)
crcl = CyRestClient()
mn.name = json.dumps(qc) if name == '' else name
cyn = crcl.network.create_from_networkx(mn)
crcl.layout.apply('kamada-kawai', network=cyn)
crcl.style.apply(Style('default'), network=cyn)
def savegraph(query, outfile, limit=4000):
"""Save IntEnz reaction connections as graph files
param: qc: MongoDB query clause to select subsets of IntEnz entries,
e.g.: \'{"reactions.label.value": ' '"Chemically balanced"}\'
param: outfile: File name for saving the output graph
Format is selected based on the file extension
of the given output file;
.xml for GraphML, .gml for GML,
.json for Cytoscape.js
param: --limit: Maximum number of enzyme-metabolite connections
"""
qry = QueryIntEnz()
qc = parseinputquery(query)
cgraph = qry.get_connections_graph(qc, int(limit / 2))
print(nx.info(cgraph))
save_graph(cgraph, outfile)
