CGView Builder

CGViewBuilder is a ruby script that generates JSON files for CGView.js from sequence files (e.g. GenBank, EMBL, FASTA).

CGViewBuilder consists of two files:

• cgview_builder.rb contains the CGViewBuilder class which can be used by other ruby programs.
• cgview_builder_cli.rb is a command line interface to the CGViewBuilder class.

Installation

• Download the git repository.
• Install CGViewBuilder's one dependency BioRuby:

gem install bio

• Confirm installation by running the test script:

./test/test.sh

Running the CLI script:

ruby cgview_builder_cli.rb [OPTIONS]

Command line options

Usage: cgview_builder_cli.rb [options]

Required Arguments:
    -s, --sequence FILE            Sequence File [GenBank for now]
    -m, --map_id STRING            ID for map [Default: Random 40 character hex string]
    -n, --map_name STRING          Name for map
    -o, --outfile FILE             Write JSON to this file

General Options:
    -c, --config FILE              Config File
    -b, --blasts FILEs             One or more blast files (separated by ,)
    -v, --version                  Print version
    -h, -?, --help                 Show this message

Config YAML

An optional config YAML can be provided to CGViewBuilder. This file will can be used to set default values for the generated JSON (e.g. colors, legends, captions, etc). See the commented example for details.