Genome processing filters and utilities

Inspired by HTML::Pipeline.

require 'genome/pipeline'

genome = Genome::Genome.new(File.open('genome.fasta'))

pipeline = Genome::Pipeline.new Filter::PRODIGAL,
                                Filter::tRNAscan

annotated_genome = pipeline[genome]

With RubyGems:

$ gem install -P HighSecurity genome-pipeline

With Bundler:

gem 'genome-pipeline'

Pipelines are made up of filters. Here is a simple filter that predicts amino-acid coding sequences using Prodigal

class ProdigalFilter < Filter

  def transform

    # run prodigal
    # read GFF and add add features to `genome`
    @result = 
      @genome.fasta do |path|
        stdin, stdout, stderr = Open3.popen3("prodigal -f gff -i #{path}")
        Features.from_gff(stdout.readlines)
      end

    super
  end
end

• Prodigal [XX]

feature finding software:

(act on genome sequence)

• Augustus
• tRNAscan
• rnammer (closed source)
• GeneMark (closed source)
• snap (no Bacterial HMM)
• prokka (see add-prokka branch)
• barrnap
• ARAGORN
• repeatscout
• repeatmasker
• trf

Filters that act on features:

• Quality Filter (remove features below a confidence threshold)

Genomes are currently read from FASTA files and stored as objects. My future plan is to save to an XML similar to NCBI GFF XML format that way the output from one filter can always be piped directly into the input of another (basically, the same way as HTML-pipeline works since HTML is just XML).

The MIT License (MIT)

Copyright (c) 2014 Austin G. Davis-Richardson

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.