class GffToProteinDBTool

Attributes

print_progress[RW]

Public Class Methods

new(option_support=[]) click to toggle source

Initializes commandline options common to all such tools. Individual search tools can add their own options, but should use Capital letters to avoid conflicts

Calls superclass method Tool::new
# File lib/protk/gff_to_proteindb_tool.rb, line 23
def initialize(option_support=[])
  super(option_support)

  if ( option_support.include? :add_transcript_info )
    add_boolean_option(:add_transcript_info,false,['--info','Include CDS Coordinates'])
  end

  @option_parser.summary_width=40

  @capturing_gene=false
  @current_gene=nil
end

Public Instance Methods

get_lines_matching(pattern,gene_lines) click to toggle source
# File lib/protk/gff_to_proteindb_tool.rb, line 46
def get_lines_matching(pattern,gene_lines)
  match_lines=[]
  gene_lines.each do |line|  
    if line =~ pattern
      match_lines << line
    end
  end
  match_lines
end
start_new_gene(line) click to toggle source
# File lib/protk/gff_to_proteindb_tool.rb, line 36
def start_new_gene(line)
  if (line =~ /maker\sgene/)
      new_gene = line.match(/ID=([^;]+)/).captures[0]
      if new_gene!=@current_gene
        @current_gene=new_gene
        return true
      end
    end
end