tpsimilarity 0.3

Package to compute TP similarities between nodes in a network.

XNET File format (xnetwork)

xnetwork is a small python package that allows you to read .xnet files (compleX NETwork format), a format designed to easily handle graph data with multiple attributes.

This file format is used across several of my other projects, including Helios-Web.

Installation

You can easily install xnetwork by using pip:

pip install xnetwork

Usage

Loading a Graph

To read a Graph from a .xnet formatted file, simply use the load function:

from xnetwork import load

graph = load("path_to_file.xnet")

Saving a Graph

To save a graph object to .xnet format:

from xnetwork import save
from igraph import Graph

# Your igraph graph object
g = Graph()

save(g, "output_file.xnet")

.xnet Format

A brief overview of the .xnet format:

#vertices <number_of_vertices>
<Vertex 0 name>
<Vertex 1 name>
...

#edges weighted|nonweighted undirected|directed
<source_vertex> <target_vertex> [weight]
...

#v "<vertex_attribute_name>" s|n|v2|v3
<attribute_value>
...

#e "<edge_attribute_name>" s|n|v2|v3
<attribute_value>
...

• The #vertices tag specifies the number of vertices in the graph, followed by their labels.

• The #edges tag specifies if edges are weighted or non-weighted and whether they are directed or undirected. Each subsequent line lists an edge by its source and target vertices, optionally followed by a weight in square brackets.

• The #v and #e tags specify vertex and edge attributes respectively. These tags are followed by the attribute name and its type. The type can be a string (s), number (n), 2D vector (v2), or 3D vector (v3).

Example

Consider the following .xnet file:

#vertices 4 
"Label 0"
"Label 1"
...
#edges weighted undirected
0 1 [0.1]
0 2 [0.2]
...
#v "A string property" s
"A string value"
"Another string value"
...

This represents a graph with 4 vertices and 2 weighted, undirected edges.

API Reference

load(fileName='test.xnet', compressed=False)

Read a Graph from a xnet formatted file.

Parameters

• fileName : string Input file path.
• compressed : bool If True, input file is compressed using gzip.

Returns

• igraph.Graph : The graph object loaded from the file.

save(g, fileName='test.xnet', ignoredNodeAtts=[], ignoredEdgeAtts=[], compressed=False)

Write igraph object to .xnet format.

Vertex attributes 'name' and 'weight' are treated in a special manner. They correspond to attributes assigned inside the #vertices tag. Edge attribute 'weight' is assigned to edges inside the #edges tag.

Parameters

• g : igraph.Graph Input graph.
• fileName : string Output file.
• ignoredNodeAtts : list List of node attributes to ignore when writing graph.
• ignoredEdgeAtts : list List of edge attributes to ignore when writing graph.
• compressed : bool If True, output file will be compressed using gzip.

Returns

• None : The function saves the graph object to the specified file.

Special network attribute names

Some attribute names are interpreted by certain software in different ways.

• Node attribute named Label is interpreted as vertex label.
• Node attribute named Position is interpreted as vertex position (can be v2 or v3).
• Node attribute named weight is interpreted as edge weight.

Authors

• Filipi N. Silva (filipinascimento.github.io)
• Cesar H. Comin

License

This project is licensed under the MIT License.

Links

• GitHub Repository

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Feel free to contribute and raise issues on the GitHub repository.