Class: Bio::Assembly::Ace::Read
Overview
extend Read class to add ace specific methods for read objects
Defined Under Namespace
Classes: BaseSequence
Instance Attribute Summary collapse
-
#base_sequences ⇒ Object
Returns the value of attribute base_sequences.
Attributes inherited from Read
#clear_range_from, #clear_range_to, #from, #name, #orientation, #seq, #to
Instance Method Summary collapse
- #add_base_sequence(from, to, read_name) ⇒ Object
- #to_ace ⇒ Object
- #to_ace_af ⇒ Object
- #to_ace_bs ⇒ Object
- #to_ace_rest ⇒ Object
Methods inherited from Read
#<=>, #==, #initialize, #num_bases
Constructor Details
This class inherits a constructor from Bio::Assembly::Read
Instance Attribute Details
#base_sequences ⇒ Object
Returns the value of attribute base_sequences.
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# File 'lib/bio-assembly/ace.rb', line 176 def base_sequences @base_sequences end |
Instance Method Details
#add_base_sequence(from, to, read_name) ⇒ Object
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# File 'lib/bio-assembly/ace.rb', line 218 def add_base_sequence(from, to, read_name) @base_sequences = Array.new if @base_sequences.nil? @base_sequences.push BaseSequence.new(from, to, read_name) end |
#to_ace ⇒ Object
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# File 'lib/bio-assembly/ace.rb', line 178 def to_ace ace += "" # holds BS data for reads bs_str = "" # holds RD, QA, and DS data for reads rest_str = "" ace += to_ace_af bs_str += to_ace_bs rest_str = to_ace_rest # compile data in correct order ace += bs_str ace += "\n" ace += rest_str ace end |
#to_ace_af ⇒ Object
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# File 'lib/bio-assembly/ace.rb', line 205 def to_ace_af ['AF', name, orientation, from].join(' ') + "\n" end |
#to_ace_bs ⇒ Object
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# File 'lib/bio-assembly/ace.rb', line 195 def to_ace_bs bs_str = "" unless base_sequences.nil? base_sequences.each do |bs| bs_str += ['BS', bs.from, bs.to, bs.read_name].join(' ') + "\n" end end bs_str end |
#to_ace_rest ⇒ Object
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# File 'lib/bio-assembly/ace.rb', line 209 def to_ace_rest rest_str = "" rest_str += ['RD', name, num_bases, 0, 0].join(' ') + "\n" rest_str += seq.to_s.gsub(Regexp.new(".{1,50}"), "\\0\n") + "\n" rest_str += ['QA', clear_range_from, clear_range_to, clear_range_from, clear_range_to].join(' ') + "\n" rest_str += ['DS', 'CHROMAT_FILE:', name, 'PHD_FILE:', "#{name}.phd.1", 'TIME:', Time.now].join(' ') + "\n" rest_str end |