Class: GffToProteinDBTool

Inherits:
Tool
  • Object
show all
Defined in:
lib/protk/gff_to_proteindb_tool.rb

Instance Attribute Summary collapse

Attributes inherited from Tool

#option_parser, #options, #options_defined_by_user

Instance Method Summary collapse

Methods inherited from Tool

#add_boolean_option, #add_default_to_help, #add_value_option, #check_options, #database_info, default_output_path, extension_from_filename, #jobid_prefix, #jobid_prefix=, #method_missing, #run, #supported_options

Constructor Details

#initialize(option_support = []) ⇒ GffToProteinDBTool

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



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# 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

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Tool

Instance Attribute Details

Returns the value of attribute print_progress.



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# File 'lib/protk/gff_to_proteindb_tool.rb', line 18

def print_progress
  @print_progress
end

Instance Method Details

#get_lines_matching(pattern, gene_lines) ⇒ Object 



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# 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) ⇒ Object 



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# 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