Class: Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser

Inherits:
TemplateParser show all
Defined in:
lib/bio/io/flatfile/indexer.rb

Overview

class MaXMLSequenceParser

Constant Summary collapse

NAMESTYLE = 
NameSpaces.new(
             NameSpace.new( 'QUERY', Proc.new { |x| x.query_def } ),
             NameSpace.new( 'query_id', Proc.new { |x| 
a = Bio::FastaDefline.new(x.query_def.to_s).id_strings
a << x.query_def.to_s.split(/\s+/,2)[0]
a
                           } ),
             NameSpace.new( 'hit', Proc.new { |x|
a = x.hits.collect { |y|
  b = Bio::FastaDefline.new(y.definition.to_s).id_strings
  b << y.definition
  b << y.definition.to_s.split(/\s+/,2)[0]
  b
}
a.flatten!
a
                           } )
)
PRIMARY = 
'QUERY'
SECONDARY = 
[ 'query_id', 'hit' ]

Instance Attribute Summary

Attributes inherited from TemplateParser

#dbclass, #errorlog, #fileid, #format, #primary, #secondary

Instance Method Summary collapse

Methods inherited from TemplateParser

#add_secondary_namespaces, #close_flatfile, #each, #parse_primary, #parse_secondary, #set_primary_namespace

Constructor Details

#initialize(klass, pri_name = nil, sec_names = nil) ⇒ BlastDefaultParser

Returns a new instance of BlastDefaultParser.



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# File 'lib/bio/io/flatfile/indexer.rb', line 392

def initialize(klass, pri_name = nil, sec_names = nil)
  super()
  self.format = 'raw'
  self.dbclass = klass
  self.set_primary_namespace((pri_name or PRIMARY))
  unless sec_names then
    sec_names = []
    @namestyle.each_value do |x|
      sec_names << x.name if x.name != self.primary.name
    end
  end
  self.add_secondary_namespaces(*sec_names)
end

Instance Method Details

#open_flatfile(fileid, file) ⇒ Object 



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# File 'lib/bio/io/flatfile/indexer.rb', line 405

def open_flatfile(fileid, file)
  super
  @flatfile.rewind
  @flatfile.dbclass = nil
  @flatfile.autodetect
  @flatfile.dbclass = self.dbclass unless @flatfile.dbclass
  @flatfile.rewind
  begin
    pos = @flatfile.pos
    line = @flatfile.gets
  end until (!line or line =~ /^T?BLAST/)
  @flatfile.pos = pos
end