Neo4j Models¶

class NetExplorer.models.neo4j_models.Document(*args, **kwargs)¶

Class for Documents uploaded to the server.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

docfile¶

The descriptor for the file attribute on the model instance. Return a FieldFile when accessed so you can write code like:

>>> from myapp.models import MyModel
>>> instance = MyModel.objects.get(pk=1)
>>> instance.file.size

Assign a file object on assignment so you can do:

>>> with open('/path/to/hello.world', 'r') as f:
...     instance.file = File(f)

id¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>¶

class NetExplorer.models.neo4j_models.Domain(accession, description=None, identifier=None, mlength=None)¶

Class for PFAM domains.

accession¶

String with accession for pfam domain (PFXXXXX).

Type: str

description¶

String with description for pfam domain.

Type: str

identifier¶

String with identifier for pfam domain.

Type: str

mlength¶

Integer with domain length.

Type: int

pfam_regexp¶

Class attribute. Regex for PFAM domain accessions.

Type: str

Parameters

accession (str) – String with accession for pfam domain (PFXXXXX).
description (str, optional) – String with description for pfam domain.
identifier (str, optional) – String with identifier for pfam domain.
mlength (int, optional) – Integer with domain length.
pfam_regexp (str, optional) – Class attribute. Regex for PFAM domain accessions.

get_planarian_contigs(database)¶

Returns a list of PlanarianContigs of ‘database’.

Parameters: database – str, database from which to retrieve the planarian contigs.
Returns: PlanarianContigs with this domain annotated.
Return type: list of PlanarianContigs
Raises: NodeNotFound – raised if there are no planarian contigs with this Domain.

classmethod is_symbol_valid(symbol)¶

Classmethod for checking if accession is a valid PFAM accession.

Parameters: symbol (str) – Symbol to check if it’s a valid PFAM accession.
Returns: True if it is valid, False otherwise.
Return type: bool

pfam_regexp = 'PF\\d{5}'

class NetExplorer.models.neo4j_models.ExperimentList(user)¶

Maps a list of experiment objects with all its available samples in the DB.

experiments¶

Set of oldExperiment instances.

Type: set of oldExperiment

samples¶

Experiments to sample names mapping. Key is experiment identifier, value is set of sample names (str).

Type: dict

datasets¶

Dictionary with list of datasets for which experiment has data for.

Type: dict

Parameters: user (models.user) – User that requests the ExperimentList.

get_datasets(experiment)¶

Returns a set for the given experiment

Parameters: experiment (str) – Experiment name.
Returns: Dataset names for which experiment has data for.
Return type: list
Raises: ExperimentNotFound – If experiment is not in ExperimentList.

get_samples(experiment)¶

Returns a set for the given experiment.

Parameters: experiment (str) – Experiment name.
Returns: Samples for which experiment has expression data for.
Return type: set
Raises: ExperimentNotFound – If experiment is not in ExperimentList.

class NetExplorer.models.neo4j_models.GeneOntology(accession, domain=None, name=None, human=False, query=True)¶

Class for GeneOntology nodes.

accession¶

GO accession, of the form “GO:…”.

Type: str

domain¶

GO domain (“molecular function”, “cellular component”, “biological process”).

Type: str

name¶

GO name.

Type: str

human_nodes¶

List of HumanNode instances that have this GO annotated.

Type: list of HumanNode

Parameters

accession (str) – GO accession, of the form “GO:…”.
domain (str, optional) – GO domain (“molecular function”, “cellular component”, “biological process”). Defaults to None
name (str, optional) – GO name. Defaults to None
human (list of HumanNode, optional) – List of HumanNode instances that have this GO annotated. Defaults to False
query (bool, optional) – Flag to query database on creation to retrieve all attributes.

_GeneOntology__query_go()¶

Query DB and get domain.

Raises: NodeNotFound – If GO does not exist in database.

get_human_genes()¶

Gets Human nodes symbols with annotated GO. Fills human_nodes attribute.

Raises: NodeNotFound – If GO does not exist in database.

get_planarian_contigs(database)¶

Gets planarian contigs whose homolog has the GO annotated. (GO)<-(Human)<-(Contig)

Parameters: database (str) – Database string from which to retrieve the PlanarianContigs.
Returns: List of PlanarianContig objects.
Return type: list

go_regexp = 'GO:\\d{7}'¶

classmethod is_symbol_valid(symbol)¶

Checks if provided symbol is a valid GO accession.

Parameters: symbol (str) – Symbol to check if it’s a valid GO accession.
Returns: True if valid, false otherwise.
Return type: bool

class NetExplorer.models.neo4j_models.GeneSearch(sterm, database)¶

Class for node/gene searches

sterm¶

Term to search.

Type: str

database¶

Database to search for sterm.

Type: str

sterm_database¶

Database to which sterm belongs to.

Type: str

Parameters

sterm (str) – Term to search.
database (str) – Database to search for sterm.

get_human_genes()¶

Returns HumanNode objects independently of the search term used.

Returns

List of HumanNode instances.: HumanNode retrieved from sterm. It is able to work with sterm of the type: ‘Human’, ‘GO’.

Return type

list of HumanNode

get_planarian_contigs()¶

Returns PlanarianContig objects that match sterm independently of the search term used.

Returns

List of PlanarianContig instances.: PlanarianContigs retrieved from sterm. It is able to work with sterm of the type: ‘Smesgene’, ‘PFAM’, ‘GO’, ‘Human’, ‘PlanarianContig’.

Return type

list of PlanarianContig

get_planarian_genes()¶

Returns PlanarianGene objects that match sterm independently of the search term used.

Returns

List of PlanarianGene instances.: PlanarianGene retrieved from sterm. It is able to work with sterm of the type: ‘Smesgene’, ‘PFAM’, ‘GO’, ‘Human’, ‘PlanarianContig’.

Return type

list of PlanarianGene

infer_symbol_database()¶: Guesses to which database sterm belongs to. Compares the symbol in sterm to the valid patterns for each NodeType. Saves result in sterm_database.

quick_search()¶

Retrieves given search term in all databases: PlanarianGene + PlanarianContigs

Returns: List of Node of the type PlanarianGene or PlanarianContig.
Return type: list of Node

class NetExplorer.models.neo4j_models.GraphCytoscape¶

Class for a graph object. Holds nodes and edges of any type as long as they have a common interface (symbol attribute and to_jsondict() method).

nodes¶

Set of Node objects.

Type: set

edges¶

Set of PredInteraction objects.

Type: set

add_elements(elements)¶

Method that takes a list of node or PredInteraction objects and adds them to the graph.

Parameters: elements (list of PredInteraction or Node) – List of PredInteraction objects or Node objects to add to the graph.
Raises: ValueError – If any element in elements is not a Node or a PredInteraction.

add_graph(graph)¶

Adds elements of graph to this graph instance.

Parameters: graph (GraphCytoscape) – Graph to be merged.

add_interaction(interaction)¶

Adds a single interaction to the graph.

Parameters: node (PredInteraction) – PredInteraction instance to add to the graph.

add_node(node)¶

Adds a single node to the graph.

Parameters: node (Node) – Node instance to add to the graph.

define_important(vip_nodes)¶

Gets a list/set of nodes and defines them as important.

Parameters: vip_nodes (list) – List of Node instances.

filter(including)¶

Filters nodes and edges from the graph.

Parameters: including (set) – Set of Node instances that has to be kept. Only interactions where both nodes are in including will be kept.

get_connections()¶: Function that looks for the edges between the nodes in the graph and adds them to the attribute edges.

get_expression(experiment, samples)¶

Gets the expression for all the node objects in the graph. Returns a dictionary: expression_data[node.symbol][sample]

Parameters

experiment (str) – :obj:`oldExperiment instance.
samples (list) – List of samples for which to get expression.

Returns

Dictionary with expression data.: Primary key is node symbol, secondary key is sample name and value is expression value (float).

Return type

dict of dict

classmethod get_genes_bulk(symbols, database)¶

Returns a dictionary of planarian genes to the specified list of planarian contig symbols from database.

Parameters

symbols (list of str) – List of node symbols.
database (str) – Database string.

Returns

Dictionary with contig-gene mapping.: Primary key is planarian contig symbol, secondary key is either ‘gene’ or ‘name’, value is gene symbol or gene name respectively.

Return type

dict of dict

classmethod get_homologs_bulk(symbols, database)¶

Returns a dictionary of homologous genes to the specified list of planarian contig symbols from database.

Parameters

symbols (list of str) – List of node symbols.
database (str) – Database string.

Returns

Dictionary with homology information.: Key is planarian contig symbol, value is human gene symbol.

Return type

dict

is_empty()¶

Checks if the graph is empty or not.

Returns: True if empty (no nodes or edges), False otherwise.
Return type: bool

new_nodes(symbols, database)¶

Takes a list of symbols and returns the necessary GraphCytoscape with Human or PlanarianContig objects

Parameters

symbols (list of str) – List of strings with gene/contig/pfam/go/kegg symbols.
database (str) – String with database.

to_json()¶

Converts the graph to a json string to add it to cytoscape.js.

Returns

JSON string with data for this graph for cytoscape.js.

Follows the structure (example):

{
    "nodes":
        [
            {
                "data":
                    {
                        "id": "dd_Smed_v6_11363_0_1",
                        "name": "dd_Smed_v6_11363_0_1",
                        "database": "Dresden",
                        "homolog": "LIG4",
                        "degree": 27,
                        "colorNODE": "#404040"
                    }
                },
            {
                "data":
                    {
                        "id": "dd_Smed_v6_9219_0_1",
                        "name": "dd_Smed_v6_9219_0_1",
                        "database": "Dresden",
                        "homolog": "FAM214A",
                        "colorNODE": "#404040"
                    },
                    "classes": "important"
                },
            }
        ],
    "edges":
        [
            {
                "data": {
                    "id": "dd_Smed_v6_11363_0_1-dd_Smed_v6_9219_0_1",
                    "source": "dd_Smed_v6_9219_0_1",
                    "target": "dd_Smed_v6_11363_0_1",
                    "pathlength": 1,
                    "probability": 0.67,
                    "colorEDGE": "#72a555"
                }
            },
        ]
}

Return type

str

class NetExplorer.models.neo4j_models.HasDomain(domain, node, p_start, p_end, s_start, s_end, perc)¶

Class for relationships between a node and a Pfam domain annotated on the sequence.

domain¶

Domain object.

Type: Domain

node¶

Node object.

Type: Node

p_start¶

Integer describing the start coordinate (1-indexed) on the PFAM domain.

Type: int

p_end¶

Integer describing the end coordinate (1-indexed) on the PFAM domain.

Type: int

s_start¶

Integer describing the start coordinate (1-indexed) on the sequence.

Type: int

s_end¶

Integer describing the end coordinate (1-indexed) on the sequence.

Type: int

perc¶

Float with % of domain in sequence.

Type: float

to_jsondict()¶

Transforms data for Sequence-Domain relationship to a JSON string.

Returns

Dictionary with JSON structure. Has the following keys:

{
    'accession': 'Domain accession',
    'description': 'Domain description',
    'identifier': 'Domain identifier',
    'mlength': 'Length (in aa) of PFAM domain',
    'p_start': 'PFAM domain start coordinate',
    'p_end': 'PFAM domain end coordinate',
    's_start': 'PFAM domain sequence start coordinate',
    's_end': 'PFAM domain sequence start coordinate',
    'perc': 'Percentage of Domain in sequence'
}

Return type

dict

class NetExplorer.models.neo4j_models.Homology(human, blast_cov=None, blast_eval=None, nog_brh=None, pfam_sc=None, nog_eval=None, blast_brh=None, pfam_brh=None, prednode=None)¶

Class for homology relationships between a PlanarianContig and a HumanNode.

human¶

Human object.

Type: Human

blast_cov¶

Float with BLAST coverage value in %.

Type: float

blast_eval¶

Float with BLAST e-value.

Type: float

blast_brh¶

Bool flag indicating if homology is best reciprocal hit in BLAST alignment.

Type: bool

nog_brh¶

Bool flag indicating if homology is best reciprocal hit in EggNOG alignment.

Type: bool

nog_eval¶

Float with EggNOG alignment e-value.

Type: float

pfam_sc¶

Float with pfam meta-alignment score.

Type: float

pfam_brh¶

Bool flag indicating if homology is best reciprocal hit in pfam alignment.

Type: bool

prednode¶

PlanarianContig object.

Type: PlanarianContig

Parameters

human (Human) – Human object.
blast_cov (float, optional) – Float with BLAST coverage value in %.
blast_eval (float, optional) – Float with BLAST e-value.
blast_brh (bool, optional) – Bool flag indicating if homology is best reciprocal hit in BLAST alignment.
nog_brh (bool, optional) – Bool flag indicating if homology is best reciprocal hit in EggNOG alignment.
nog_eval (float, optional) – Float with EggNOG alignment e-value.
pfam_sc (float, optional) – Float with pfam meta-alignment score.
pfam_brh (bool, optional) – Bool flag indicating if homology is best reciprocal hit in pfam alignment.
prednode (PlanarianContig, optional) – PlanarianContig object.

class NetExplorer.models.neo4j_models.HumanNode(symbol, database, query=True)¶

Human node class definition. Inherits from ‘Node’.

summary¶: String with gene summary.

summary_source¶: String with the source of the summary.

allowed_databases = {'Human'}¶

get_homologs(database='ALL')¶

Gets all homologs of the specified database.

Parameters

database (str) – Database of desired homologous planarian contigs. Defaults to “ALL”.

Returns

Dictionary with homologous contigs to HumanNode.

{
    'database1': [Homology, Homology, ...],
    ...
}

Return type

dict

get_neighbours()¶: Gets HumanNodes that interact with this HumanNode. Not implemented yet.

get_planarian_contigs(database)¶

Gets all PlanarianContigs homologous to HumanNode.

Parameters: database (str) – Database from which to retrieve planarian contigs.
Returns: PlanarianContig objects.
Return type: list

get_planarian_genes(database)¶

Gets planarian gene objects (PlanarianGene) connected to HumanNode through contigs of dataset ‘database’, i.e.: (:Human)->(:Database)->(:Smesgene)

Parameters: database (str) – Database of contigs to get PlanarianGene
Returns: List of PlanarianGene instances.
Return type: list

get_summary()¶: Retrieves gene summary when available and saves it into attribute.

to_jsondict()¶

Serializes HumanNode to a dictionary for converting it to JSON.

Returns

Serialized HumanNode.

{
    'data':
        {
            'id': 'node identifier',
            'name': 'node name',
            'database': 'Human'
        }
}

Return type

dict

class NetExplorer.models.neo4j_models.KeggPathway(symbol, database)¶

Class for KeggPathways. Encapsulates a GraphCytoscape object in graphelements. Will query Kegg on creation.

symbol¶

Symbol for Kegg Pathway.

Type: str

database¶

Planarian database to which this KeggPathway will be mapped to.

Type: str

kegg_url¶

Url to the pathway in Kegg.

Type: str

graphelements¶

GraphCytoscape object that results from looking at the genes and interactions in the Pathway that appear in the neo4j database.

Type: GraphCytoscape

Parameters

symbol (str) – Symbol for Kegg Pathway.
database (str) – Planarian database to which this KeggPathway will be mapped to.

get_graph_from_kegg()¶

Connects to KEGG and extracts the elements of the pathway.

Returns

GraphCytoscape object that results from: looking at the genes and interactions in the Pathway that appear in the neo4j database. If Kegg can’t be reached or the pathway does not have any equivalent in PlanNET, the GraphCytoscape will be empty.

Return type

GraphCytoscape

class NetExplorer.models.neo4j_models.Node(symbol, database)¶

Base class for all the nodes in the database.

symbol¶

String containing the symbol attribute in Neo4j of a given node.

Type: str

database¶

The Label for the symbol in Neo4j.

Type: str

neighbours¶

List of Interaction objects connecting nodes adjacent to the Node.

Type: list of PredInteraction

domains¶

HasDomain objects describing domains in the sequence/node.

Type: list of HasDomain

allowed_databases¶

Class attribute. Set of allowed Labels for Node.

Type: set of str

_Node__query_node()¶: This method will be overriden by HumanNode or PlanarianContig. It will query the Neo4j database and it will get the required node.

domains_to_json()¶

This function will return a json string with the information about the domains of the node. You have to call “get_domains()” before!

Returns: JSON string with Domains data, see Domain.to_jsondict().
Return type: str

get_domains()¶

Gets domains annotated for a particular Node. It updates the Node attribute and it also returns the domain.

Returns: List of domains annotated for this Node. None if there are no domain annotations.
Return type: Union([list of Domain, None])

class NetExplorer.models.neo4j_models.Pathway(graph)¶

Class for pathways. They are basically GraphCytoscape objects with score property.

graph (: obj:`GraphCytoscape): Graphcytoscape object of the pathway.

Parameters: ( (graph) – obj:`GraphCytoscape): Graphcytoscape object of the pathway.

score¶

Mean score of interactions in pathway.

Type: float

class NetExplorer.models.neo4j_models.PlanarianContig(symbol, database, sequence=None, name=None, gene=None, orf=None, homolog=None, important=False, degree=None, query=True)¶

Class for planarian nodes.

Parameters

symbol (str) – Node symbol.
database (str) – Label for Neo4j.
sequence (str) – Contig nucleotide sequence.
orf (str) – Open Reading Frame aa sequence.
name (str) – Name of the contig according to its gene annotation.
gene (PlanarianGene) – Gene predicted to have this transcript as a product.
homolog (Homology) – Homology object with human homolog gene.
important (bool) – Bool indicating if Node should be marked on graph visualization. Defaults to False.
degree (int) – Integer with the degree (number of connections) of the node.
query (bool) – Flat to indicate if database should be queried. Defaults to False.

symbol¶

Node symbol.

Type: str

database¶

Label for Neo4j.

Type: str

sequence¶

Contig nucleotide sequence.

Type: str

orf¶

Open Reading Frame aa sequence.

Type: str

orflength¶

Length of Open Reading Frame.

Type: int

gccount¶

% of GC in contig sequence.

Type: float

gene_ontologies¶

List of GeneOntology objects that its HumanNode has annotated.

Type: list

name¶

Name of the contig according to its gene annotation.

Type: str

gene¶

Gene predicted to have this transcript as a product.

Type: PlanarianGene

homolog¶

Homology object with human homolog gene.

Type: Homology

important¶

Bool indicating if Node should be marked on graph visualization. Defaults to False.

Type: bool

degree¶

Integer with the degree (number of connections) of the node.

Type: int

allowed_databases¶

Class attribute, dictionary with names of neo4j labels for planarian genes.

Type: dict

_PlanarianContig__query_node()¶

Gets node from neo4j and fills sequence, orf, length and homology attributes.

Raises: NodeNotFound – If node is not in database.

allowed_databases = {'Adamidi', 'Blythe', 'Consolidated', 'Cthulhu', 'Dresden', 'Gbrna', 'Graveley', 'Illuminaplus', 'Pearson', 'Smed454', 'Smedgd', 'Smest'}

get_all_information()¶: Fills all attributes of PlanarianContig by querying the database

get_expression(experiment, sample)¶: Gets expression data for a particular node, a particular experiment and a particular sample

get_gene_name()¶: Gets gene name if possible and loads gene and name attributes.

get_geneontology()¶: Gets Gene Ontologies of the homologous human protein.

get_genes()¶

Gets Genes to which this contig maps.

Returns

List of PlanarianGene objects that this contig is: associated with.

Return type

list

get_graphelements(including=None)¶: Returns a list of nodes and edges adjacent to the node.

get_homolog()¶: Tries to get the homologous human gene of this planarian transcript

get_neighbours()¶: Method to get the adjacent nodes in the graph and all the information about those connections (including the homology information, etc.). Fills attribute neighbours, which will be a list of PredInteraction objects.

get_neighbours_shallow()¶: Method to get adjacent nodes (and their degree) in the graph without homology information and only with path_length and probability for the interaction information. It also retrieves the degree of the neighbour nodes. Fills attribute neighbours, which will be a list of PredInteraction objects. Used by NetExplorer add_connection/expand

get_summary()¶: Fills attribute values that are not mandatory, with a summary of several features of the node. Fills attributes “length” and “orflength”.

path_to_node(target, plen)¶

Given a target node object, this method finds all the shortest paths to that node of length plen. If there aren’t any, it returns None.

Parameters

target (PlanarianContig) – Target gene in the graph.
plen (int) – Path length to consider. All paths from self to target will be of length = `plen.

Returns

Pathway between self and target or None if no pathway exists.

Return type

Union([Pathway, None])

to_jsondict()¶

This function takes a node object and returns a dictionary with the necessary structure to convert it to json and be read by cytoscape.js

Returns

Dictionary with serialized PlanarianContig.

{
    'data':
        {
            'id': 'contig id',
            'name': 'contig name',
            'database': 'contig database',
            'homolog': 'human homolog symbol',
            'degree': int,
            'colorNode': '#404040',
        },
    'classes': 'null or important'

}

Return type

dict

class NetExplorer.models.neo4j_models.PlanarianGene(symbol, database, name=None, start=None, end=None, strand=None, sequence=None, homolog=None, chromosome=None, query=True)¶

Class for PlanarianGenes (genes from Planmine 3.0 gene annotation)

symbol¶

Gene symbol (SMESG…).

Type: str

database¶

‘Smesgene’.

Type: str

name¶

Gene name (if any).

Type: str

start¶

Start coordinate in chromosome.

Type: int

end¶

End coordinate in chromosome.

Type: int

strand¶

Strand in chromosome (+1: Forward , -1: Reverse)

Type: int

sequence¶

Nucleotide sequence of gene.

Type: str

homolog¶

Homologous gene.

Type: HumanNode

chromosome¶

Chromosome name where gene is located.

Type: str

Parameters

symbol (str) – Gene symbol (SMESG…).
database (str) – ‘Smesgene’.
name (str, optional) – Gene name (if any). Defaults to None.
start (int) – Start coordinate in chromosome. Defaults to None.
end (int, optional) – End coordinate in chromosome. Defaults to None.
strand (int, optional) – Strand in chromosome (+1: Forward , -1: Reverse). Defaults to None.
sequence (str, optional) – Nucleotide sequence of gene. Defaults to None.
homolog (HumanNode, optional) – Homologous gene. Defaults to None.
chromosome (str, optional) – Chromosome name where gene is located. Defaults to None.
query (bool, optional) – Flag to decide if gene should be queried on creation. Defaults to False.

_PlanarianGene__query_node()¶

Queries PlanarianGene to get and fill the attributes from the database.

Raises: NodeNotFound – If gene is not in database.

allowed_databases = {'Smesgene'}¶

get_best_transcript()¶

Retrieves the longest transcript of preferred_database.

Returns

PlanarianContig from preferred database annotated: as being transcribed from this gene.

Return type

PlanarianContig

get_homolog()¶

Gets homologous gene of longest transcript associated with this PlanarianGene. Fills attribute ‘homolog’. Returns the HumanNode object.

Returns: Homologous HumanNode if there is any, otherwise None.
Return type: HumanNode or None

get_planarian_contigs(database=None)¶

Returns list PlanarianContig objects of database or all databases that map to the PlanarianGene genomic location.

Parameters

database (str, optional) – Database from which to retrieve planarian contigs. if not defined will get planarian contigs from all databases.

Returns

PlanarianContig objects associated with this: gene.

Return type

list of PlanarianContig

classmethod is_symbol_valid(symbol)¶

Checks if symbol is valid

Parameters: symbol (str) – Symbol to check if follows PlanarianGene naming convention.
Returns: True if symbol is a valid gene identifier. False otherwise.
Return type: bool

preferred_database = 'Smest'¶

smesgene_regexp = 'SMESG\\d+'¶

class NetExplorer.models.neo4j_models.PredInteraction(source_symbol, target, database, parameters=None, query=True)¶

Class for predicted interactions. Source and target are PlanarianContig attributes.

source_symbol¶

Symbol of parent node of interaction.

Type: str

target¶

Node object of the child node of the interaction.

Type: Node

database¶

Neo4j label of parent and child nodes.

Type: str

parameters¶

Dictionary containing the interaction properties. Has following structure:

{
    'int_prob': float,
    'path_length': int,
    'cellcom_nto': float,
    'molfun_nto': float,
    'bioproc_nto': float,
    'dom_int_sc': float
}

Type: dict

Parameters

source_symbol (str) – Symbol of parent node of interaction.
target (Node) – Node object of the child node of the interaction.
database (str) – Neo4j label of parent and child nodes.

parameters (dict, optional) –

Dictionary containing the interaction properties. Defaults to None:

{
    'int_prob': float,
    'path_length': int,
    'cellcom_nto': float,
    'molfun_nto': float,
    'bioproc_nto': float,
    'dom_int_sc': float
}

query (bool) – Bool flag indicating if interaction should be queried to database on creation. Defaults to True. Query will only be performed if query = True and parameters = None.

_PredInteraction__query_interaction()¶: This private method will fetch the interaction from the DB. It will fill the attributes [‘int_prob’, ‘path_length’, ‘cellcom_nto’, ‘molfun_nto’, ‘bioproc_nto’, ‘dom_int_sc’] of the PredInteraction instance. If interaction is not found, they all will be None.

to_jsondict()¶

This function takes a PredInteraction object and returns a dictionary with the necessary structure to convert it to json and be read by cytoscape.js.

Returns

Serialized PredInteraction.

{
    'data':
        {
            'id': 'edge identifier',
            'source': 'node identifier',
            'target': 'node identifier',
            'pathlength': int,
            'probability': float,
            'colorEdge': 'HEX color code',
        }
}

Return type

dict

class NetExplorer.models.neo4j_models.WildCard(search, database)¶

Class for wildcard searches. Returns a list of symbols.

Parameters

search (str) – String to search.
database (str) – Database (label in neo4j) for the search.

search¶

String to search.

Type: str

database¶

Database (label in neo4j) for the search.

Type: str

get_human_genes()¶

Gets list of HumanNode objects matching the wildcard query.

Returns: HumanNode objects.
Return type: list

get_planarian_genes()¶

Gets list of PlanarianGene objects matching the wildcard query.

Returns: PlanarianGene objects.
Return type: list

class NetExplorer.models.neo4j_models.oldExperiment(identifier, url=None, reference=None)¶

Legacy class for gene expresssion experiments. Mantained until PlanExp is published.

id¶

Experiment identifier.

Type: str

url¶

Experiment publication URL.

Type: str

reference¶

Formatted publication reference.

Type: str

minexp¶

Minimum expression value in whole experiment.

Type: float

maxexp¶

Maximum expression value in whole experiment.

Type: float

percentiles¶

List of floats indicating the expression value at each percentile (15 in total).

Type: list of int

Parameters

id (str) – Experiment identifier.
url (str, optional) – Experiment publication URL. If not passed on creation, will query the database to get the data for this experiment.
reference (str, optional) – Formatted publication reference.

_oldExperiment__get_minmax()¶: Checks if the specified experiment exists in the database and gets the max, min expression ranges and the reference defined.

color_gradient(from_color, to_color, comp_type)¶

This method returns a color gradient of length bins from “from_color” to “to_color”.

Parameters

from_color (str) – Hex value of initial color for gradient.
to_color (str) – Hex value of final color for gradient.
comp_time (str) – “one-sample” or “two-sample”, indicating if gradient should be linear (“one-sample”) or divergent “two-sample”.

to_json()¶

Returns a json string with the info about the experiment.

Returns

JSON string with the following structure.

{
    'data':
        {
            'id': 'experiment identifier',
            'url': 'url of experiment' ,
            'reference': 'formatted reference',
            'minexp': float,
            'maxexp': float,
            'percentiles': [ float, float, float, ...]

        }
}

Return type

str