Class: Bio::Blast::RPSBlast::RPSBlastSplitter

Inherits:
FlatFile::Splitter::Template show all
Defined in:
lib/bio/appl/blast/rpsblast.rb

Overview

Flatfile splitter for RPS-BLAST reports. It is internally used when reading RPS-BLAST report. Normally, users do not need to use it directly.

Note for Windows: RPS-BLAST results generated in Microsoft Windows may not be parsed correctly due to the line feed code problem. For a workaroud, convert line feed codes from Windows(DOS) to UNIX.

Constant Summary collapse

ReportHead =

Separator used to distinguish start of each report

/\A\n*(RPS\-BLAST|Query\=)/
Delimiter =

Delimiter used for IO#gets

"\n\n"

Instance Attribute Summary

Attributes inherited from FlatFile::Splitter::Template

#entry, #entry_ended_pos, #entry_pos_flag, #entry_start_pos, #parsed_entry

Instance Method Summary collapse

Methods inherited from FlatFile::Splitter::Template

#get_parsed_entry

Constructor Details

#initialize(klass, bstream) ⇒ RPSBlastSplitter

creates a new splitter object



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# File 'lib/bio/appl/blast/rpsblast.rb', line 54

def initialize(klass, bstream)
  super(klass, bstream)
  @entry_head = nil
end

Instance Method Details

#get_entry ⇒ Object

gets an entry



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# File 'lib/bio/appl/blast/rpsblast.rb', line 73

def get_entry
  p0 = stream_pos()
  pieces = []
  flag_head = false # reached to start of header
  flag_body = false # reached to start of body (Query=...)
  while x = stream.gets(Delimiter)
    if ReportHead =~ x then
      case $1
      when 'RPS-BLAST'
        if pieces.empty? then
          @entry_head = nil
          flag_head = true
        else
          stream.ungets(x)
          break
        end
      when 'Query='
        if flag_body then
          stream.ungets(x)
          break
        else
          @entry_head = pieces.join('') if flag_head
          flag_body = true
        end
      else
        raise 'Bug: should not reach here'
      end
    end #if ReportHead...
    pieces.push x
  end #while
  p1 = stream_pos()

  self.entry_start_pos = p0
  self.entry = 
    if pieces.empty? then
      nil
    elsif !flag_head and @entry_head then
      @entry_head + pieces.join('')
    else
      pieces.join('')
    end
  self.entry_ended_pos = p1
  return self.entry
end

#rewind ⇒ Object

Rewinds the stream



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# File 'lib/bio/appl/blast/rpsblast.rb', line 67

def rewind
  @entry_head = nil
  super
end

#skip_leader ⇒ Object

Skips leader of the entry. In this class, only skips space characters.



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# File 'lib/bio/appl/blast/rpsblast.rb', line 61

def skip_leader
  stream.skip_spaces
  return nil
end