bio-cd-hit-report

A bioruby wrapper for parsing and reading CD-HIT cluster reports

Note: this software is under active development!

Installation

    gem install bio-cd-hit-report

Usage

  require 'bio-cd-hit-report'

   cluster_file = "cluster95.clstr"
    report = Bio::CdHitReport.new(cluster_file)

      #print the max number of sequences in a cluster for the entire dataset
      puts report.max_members 

      #print the minimum number of sequences in a cluster for the entire dataset
      puts report.min_members 

      #print total number of clusters in the report
      puts report.total_clusters  

      #print the cluster members for cluster with id 1
      puts report.get_cluster(1)

      #information for each cluster
      report.each_cluster do |c|
        puts "#{c.name} - #{c.members}" #print cluster name/id with respective sequences in the cluster
        puts c.size #print the total number of entries in the cluster
      end

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/georgeG/bioruby-cd-hit-report

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Cite

If you use this software, please cite one of

Biogems.info