def go_annotations(dburl=config.get("databases.go_url",None), genus="Saccharomyces", species="cerevisiae", include_ancestors=False):
"""Accesses GO annotations in a MySQL database.
Database data can be obtained from the geneontology website.
example url: "mysql://username:password@hostname:port/go
"""
go = open_go(dburl)
g = go.species |Match(_.id, _.species_id)| go.gene_product
g = g |Match(_.gene_product.id, _.gene_product_id)| go.association
g = g |Match(_.association.id, _.association_id)| go.evidence
g = g |Match(_.gene_product.dbxref_id, _.id)| go.dbxref
if include_ancestors:
g = g |Match(_.association.term_id, _.term2_id)| go.graph_path
g = g |Match(_.term1_id, _.id)| go.term//"annot"
g = g |Match(_.relationship_type_id, _.id)| go.term//"rel"
g = g[_.rel.name == "is_a"]
else:
g = g |Match(_.association.term_id, _.id)| go.term//"annot"
g = g[(_.genus==genus) & (_.species == species)][_.is_not == False][_.evidence.code != "ND"]
g = g.ReplaceMissing()
g = g.Get(_.symbol /"gene_symbol", _.xref_key / "gene_id",
_.annot.acc/"go_id", _.annot.name/"annotation", _.annot.term_type/"go_type",
_.evidence.code/"evidence")%"annotations"
return g.Copy()
def string_interaction_types(dburl=config.get('databases.string_url',None), species="Saccharomyces cerevisiae", external_names=False):
"""Given a Postgres db with String data, specified in dburl, and a species, returns all interactions and their score.
The database data can be obtained from String.
example url: "postgres://*****:*****@hostname:port/string_dbname"
Use ``connect`` to access the whole database::
#Get available species names:
>>> connect(dburl).items.species.offical_name
"""
z = string(dburl)
inter = z.network.actions
inter = inter |Match(_.item_id_a, _.protein_id)| z.items.proteins//"left"
inter = inter |Match(_.item_id_b, _.protein_id)| z.items.proteins//"right"
inter = inter |Match(_.left.species_id, _.species_id)| z.items.species
inter = inter[_.official_name == species]
if external_names:
names = inter.Get(_.left.protein_external_id/"left", _.right.protein_external_id/"right").Each(lambda x : x.split('.')[1],dtype="bytes")
else:
names = inter.Get(_.left.preferred_name/"left", _.right.preferred_name/"right")
return inter.Get(names,
_.mode, _.action, _.a_is_acting,
_.score) % "interactions"
def string_interactions(dburl=config.get('databases.string_url',None), species="Saccharomyces cerevisiae", subscores=False, external_names=False):
"""Given a Postgres db with String data, specified in dburl, and a species, returns all interactions and their score.
The database data can be obtained from String.
example url: "postgres://*****:*****@hostname:port/string_dbname"
Use ``connect`` to access the whole database::
#Get available species names:
>>> connect(dburl).items.species.offical_name
"""
z = string(dburl)
inter = z.items.species |Match| z.network.protein_protein_links
inter = inter[_.official_name == species]
inter = inter |Match(_.protein_id_a, _.protein_id)| z.items.proteins//"left"
inter = inter |Match(_.protein_id_b, _.protein_id)| z.items.proteins//"right"
if external_names:
names = inter.Get(_.left.protein_external_id/"left", _.right.protein_external_id/"right").Each(lambda x : x.split('.')[1],dtype="bytes")
else:
names = inter.Get(_.left.preferred_name/"left", _.right.preferred_name/"right")
if(subscores):
return inter.Get(names,
_.equiv_nscore/"neighborhood_score", _.equiv_nscore_transferred/"neighborhood_score_transferred",
_.equiv_fscore/"fusion_score",
_.equiv_pscore/"phylo_cooccurence_score",
_.equiv_hscore/"homology_score",
_.array_score/"coexpression_score",
_.array_score_transferred/"coexpression_score_transferred",
_.experimental_score/"experimental_score",
_.experimental_score_transferred/"experimental_score_transferred",
_.database_score/"curated_score",
_.database_score_transferred/"curated_score_transferred",
_.textmining_score/"textmining_score",
_.textmining_score_transferred/"textmining_score_transferred",
_.combined_score) % "interactions"
else:
return inter.Get(names,
_.combined_score) % "interactions"
def go_info(dburl=config.get("databases.go_url",None), genus="Saccharomyces", species="cerevisiae", include_ancestors=False):
"""Accesses GO term info in a MySQL database.
Database data can be obtained from the geneontology website.
example url: "mysql://username:password@hostname:port/go
"""
go = open_go(dburl)
#select annotations from a certain species, and their ancestor annotations
g = go.species
g = g |Match(_.id, _.species_id)| go.gene_product
g = g |Match(_.gene_product.id, _.gene_product_id)| go.association
g = g |Match(_.association.term_id, _.term2_id)| go.graph_path
g = g[(_.genus==genus) & (_.species == species)]
#link them to terms to get actual go accession id
g = g |Match(_.term2_id, _.id)| go.term//"child"
g = g |Match(_.term1_id, _.id)| go.term//"parent"
g = g |Match(_.relationship_type_id, _.id)| go.term//"rel"
#get relevant fields
g = g.ReplaceMissing()
if include_ancestors:
g = g.Get(_.child.acc/"go_id", _.parent.acc/"parent_id", _.gene_product.id/"gene_id").Copy()
else:
g = g.Get(_.child.acc/"go_id", _.parent.acc/"parent_id", _.child.term_type/"go_type", _.child.name/"annotation",
_.distance, _.rel.name/"relationship", _.gene_product.id/"gene_id").Copy()
#step A: calculate number of genes associated with go terms
ngenes = g.GroupBy(_.parent_id).Get(_.parent_id/"go_id",_.gene_id.Unique().Count()/"ngenes")
if include_ancestors:
g2 = go.graph_path
g2 = g2 |Match(_.term2_id, _.id)| go.term//"child"
g2 = g2 |Match(_.term1_id, _.id)| go.term//"parent"
g2 = g2 |Match(_.relationship_type_id, _.id)| go.term//"rel"
g2 = g2.Get(_.child.acc/"go_id", _.parent.acc/"parent_id", _.child.term_type/"go_type", _.child.name/"annotation",
_.distance, _.rel.name/"relationship").Copy()
#step B1: group per term
g2 = g2[_.go_id |In| ngenes.go_id]
goinfo = g2.GroupBy(_.go_id, flat=(_.go_type, _.annotation))
#step B2: for ech term, determine type, max depth to root, ancestors (non-unique) and relationship to ancestors
goinfo = goinfo.Get(_.go_id, _.go_type, _.annotation,
_[_.parent_id == "all"].distance.Max()/"depth",
_.parent_id / "ancestor", _.relationship, _.distance)
#step B3: select for each ancestor the minimum path length
goinfo = goinfo.GroupBy(_.ancestor)[..., _.distance.Argmin()].Copy()
else:
#step B1: group per term
goinfo = g.GroupBy(_.go_id, flat=(_.go_type, _.annotation))
#step B2: for ech term, determine type, max depth to root, ancestors (non-unique) and relationship to ancestors
goinfo = goinfo.Get(_.go_id, _.go_type, _.annotation,
_[_.parent_id == "all"].distance.Max()/"depth",
_.parent_id / "ancestor", _.relationship, _.distance)
#step B3: select for each ancestor the minimum path length
goinfo = goinfo.GroupBy(_.ancestor)[..., _.distance.Argmin()].Copy()
#step C: combine, copy, return
return (goinfo |Match| ngenes).Copy()
def open_go(dburl=config.get("databases.go_url",None)):
go = Connect(dburl)
return go
def string(dburl=config.get('databases.string_url',None)):
return Connect(dburl)
def run(cls, query, run_manager, portnumber=config.get('debug.cytoscape_port_number',9000)):
self = cls()
self.rand = random.randint(0,10000000)
self.graph = run_manager.pass_results[create_graph.CreateGraph]
self.graph.pruneGraph()
self.server = xmlrpclib.ServerProxy("http://localhost:" + str(portnumber)).Cytoscape
self.network = self.server.createNetwork("network" + str(networkid()))
self.unique_names = defaultdict(int)
self.names = dict()
self.node_name = dict()
self.node_class = dict()
self.node_type = dict()
self.node_rep = dict()
self.edge_from = []
self.edge_to = []
self.edge_type = []
self.edge_attr = []
for node in self.graph.nodes:
self.node(node)
self.server.createNodes(self.network, self.names.values())
for source,edges in self.graph.edge_source.iteritems():
for edge in edges:
assert edge.source is source, "Source in edge and index not equal"
self.edgeKey(edge.__class__.__name__,edge)
self.edgeids = self.server.createEdges(self.network,self.edge_from, self.edge_to, self.edge_type,[True] * len(self.edge_type),False)
self.server.addNodeAttributes("name","STRING",self.node_name,False)
self.server.addNodeAttributes("type","STRING",self.node_type,False)
self.server.addNodeAttributes("class","STRING",self.node_class,False)
self.server.addNodeAttributes("rep","STRING",self.node_rep,False)
self.server.addEdgeAttributes("type","STRING",dict(zip(self.edgeids,self.edge_type)))
self.server.addEdgeAttributes("attr","STRING",dict(zip(self.edgeids,self.edge_attr)))
for attribute,attribute_dict in self.graph.node_attributes.iteritems():
attribute_name_dict = {}
if(isinstance(attribute_dict.values()[0], float)):
xtype = "FLOATING"
cls = float
elif(isinstance(attribute_dict.values()[0], int)):
xtype = "INTEGER"
cls = int
else:
xtype = "STRING"
cls = str
for node, node_name in self.names.iteritems():
try:
r = attribute_dict.get(node,"")
if(isinstance(r, representor.Representor)):
r = str(r.__class__.__name__)
else:
r = cls(r)
if isinstance(r,str) and len(r) > 500:
r = r[:500] + ' ...'
attribute_name_dict[node_name] = r
except:
pass
self.server.addNodeAttributes(attribute,xtype,attribute_name_dict,False)
if(attribute == 'links'):
import matplotlib.cm
cm = discrete_color_map(attribute_name_dict.values(), matplotlib.cm.gist_rainbow)
self.server.createDiscreteMapper('default','links', 'Node Color','#444444',cm)
if(attribute == "time"):
self.server.createContinuousMapper('default','time', 'Node Size',[0.0, max(attribute_dict.values())],[20.0, 20.0, 100.0, 100.0])
self.server.setNodeLabel(self.network, "name", "","default")
self.server.setDiscreteNodeShapeMapper(self.network, 'default',
'type', 'diamond', {'else':'ellipse', 'unaryop':'octagon', 'rep':'round_rect'}, True)
self.server.setEdgeTargetArrowRule(self.network,"type","Arrow",["ParamListEdge","ParamChoiceListEdge"],["T","T"])
self.server.setEdgeLineStyleRule(self.network,"type","SOLID",["ParamChoiceEdge","ParamChoiceListEdge",'SQLResultEdge'],["DOT","DOT","SINEWAVE"])
self.server.performLayout(self.network, "hierarchical")