Module: Bio::PL::GFF3

Defined in:
lib/bio-gff3-pltools/filtering.rb,
lib/bio-gff3-pltools/validation.rb

Class Method Summary collapse

Class Method Details

.filter_data(data, filter_string, options = {}) ⇒ Object

Runs the gff3-ffetch utility with the specified parameters while passing data to its stdin. Options include :output and :at_most, :keep_fasta, :keep_comments, :keep_pragmas, :gtf_output, :json_output, :select



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# File 'lib/bio-gff3-pltools/filtering.rb', line 52

def self.filter_data data, filter_string, options = {}
  output_option = nil
  output = nil
  if !options[:output].nil?
    output_option = "--output #{options[:output]}"
  end
  if !options[:at_most].nil?
    at_most_option = "--at-most #{options[:at_most]}"
  end
  if options[:keep_fasta]
    fasta_option = "--keep-fasta"
  end
  if options[:keep_comments]
    comments_option = "--keep-comments"
  end
  if options[:keep_pragmas]
    pragmas_option = "--keep-pragmas"
  end
  if options[:gtf_output]
    gtf_output_option = "--gtf-output"
  end
  if options[:json_output]
    json_output_option = "--json"
  end
  if !options[:select].nil?
    select_option = "--select \"#{options[:select]}\""
  end
  gff3_ffetch = IO.popen("gff3-ffetch --filter \"#{filter_string}\" - #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gtf_output_option} #{json_output_option} #{select_option}", "r+")
  gff3_ffetch.write data
  gff3_ffetch.close_write
  if output_option.nil?
    output = gff3_ffetch.read
  end
  gff3_ffetch.close
  output
end

.filter_file(filename, filter_string, options = {}) ⇒ Object

Runs the gff3-ffetch utility with the specified parameters on an external file. Options include :output, :at_most, :keep_fasta, :keep_comments, :keep_pragmas, :gtf_output, :json_output, :select



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# File 'lib/bio-gff3-pltools/filtering.rb', line 8

def self.filter_file filename, filter_string, options = {}
  if !File.exists?(filename)
    raise Exception.new("No such file - #{filename}")
  end

  output_option = nil
  output = nil
  if !options[:output].nil?
    output_option = "--output #{options[:output]}"
  end
  if !options[:at_most].nil?
    at_most_option = "--at-most #{options[:at_most]}"
  end
  if options[:keep_fasta]
    fasta_option = "--keep-fasta"
  end
  if options[:keep_comments]
    comments_option = "--keep-comments"
  end
  if options[:keep_pragmas]
    pragmas_option = "--keep-pragmas"
  end
  if options[:gtf_output]
    gtf_output_option = "--gtf-output"
  end
  if options[:json_output]
    json_output_option = "--json"
  end
  if !options[:select].nil?
    select_option = "--select \"#{options[:select]}\""
  end
  puts "gff3-ffetch --filter \"#{filter_string}\" #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gtf_output_option} #{json_output_option} #{select_option}"
  gff3_ffetch = IO.popen("gff3-ffetch --filter \"#{filter_string}\" #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option} #{gtf_output_option} #{json_output_option} #{select_option}")
  if output_option.nil?
    output = gff3_ffetch.read
  end
  gff3_ffetch.close
  output
end

.validate_file(filename) ⇒ Object

Runs the gff3-validate utility with the specified filename as argument. Returns error messages if the utility found issues in the file.



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# File 'lib/bio-gff3-pltools/validation.rb', line 7

def self.validate_file filename
  if !File.exists?(filename)
    raise Exception.new("No such file - #{filename}")
  end

  gff3_validate = IO.popen(["gff3-validate", "#{filename}", :err=>[:child, :out]])
  output = gff3_validate.read
  gff3_validate.close
  output
end