cxtool

README

cxtool: CX File Utility

Introduction

This is a file conversion utility for CX. Main function of this tool is data format conversion from/to SIF, Cytoscape.js JSON and many others.

Status

• 5/5/2016: Repository moved to cyService.
• 11/20/2015: Pre alpha. Simply converts CX to basic Cytoscpae.js JSON.

Build

In addition to build executables, you need to generate

• https://github.com/jteeuwen/go-bindata

Run:

go-bindata -o converter/ data/

to generate new bundle. And copy it to

Supported Functions

• From CX

  • Cytoscape.js (both Style and Graph)

• To CX

  • SIF (Simple Interaction Format)
  • Cytoscape.js (ONGOING)
  • MITAB (TODO)
  • GraphML (TODO)

How to Use

This is a small collection of tools to support round-trip for CX and related documents.

Basic Usage

1. Show Help

cxtool -h

Or simply

cxtool

1. Convert CX file into Cytoscape.js

cxtool input_file

We recommend to install jq for generating human-friendly output.

The following command creates nicely formatted Cytoscape.js JSON.

cxtool input_file | jq

Or, use pipe for input

cat network.cx | cxtool | jq .
curl http://example.com/network.cx | cxtool | jq . > cytoscapejs1.json

1. Create CX from SIF

cxtool -f sif galFiltered.sif | jq | from_sif.cx

Command Line Options

(TBD)

License

MIT License

Question?

Please send your question to (kono at ucsd edu).

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© 2015 The Cytoscape Consortium

Documentation

Overview

cxtool: A command line tool to convert CX and related files

by Keiichiro Ono (kono at ucsd edu)

(c) 2015 - 2016 The Cytoscape Consortium

MIT License