class Bio::Blast::RPSBlast::Report::FLATFILE_SPLITTER

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.

Constants

Delimiter: Delimiter used for IO#gets
ReportHead: Separator used to distinguish start of each report

Public Class Methods

new (klass, bstream)

Source

   # File lib/bio/appl/blast/rpsblast.rb
54 def initialize(klass, bstream)
55   super(klass, bstream)
56   @entry_head = nil
57 end

creates a new splitter object

Calls superclass method Bio::FlatFile::Splitter::Template::new

Public Instance Methods

get_entry ()

Source

    # File lib/bio/appl/blast/rpsblast.rb
 73 def get_entry
 74   p0 = stream_pos()
 75   pieces = []
 76   flag_head = false # reached to start of header
 77   flag_body = false # reached to start of body (Query=...)
 78   while x = stream.gets(Delimiter)
 79     if ReportHead =~ x then
 80       case $1
 81       when 'RPS-BLAST'
 82         if pieces.empty? then
 83           @entry_head = nil
 84           flag_head = true
 85         else
 86           stream.ungets(x)
 87           break
 88         end
 89       when 'Query='
 90         if flag_body then
 91           stream.ungets(x)
 92           break
 93         else
 94           @entry_head = pieces.join('') if flag_head
 95           flag_body = true
 96         end
 97       else
 98         raise 'Bug: should not reach here'
 99       end
100     end #if ReportHead...
101     pieces.push x
102   end #while
103   p1 = stream_pos()
104 
105   self.entry_start_pos = p0
106   self.entry = 
107     if pieces.empty? then
108       nil
109     elsif !flag_head and @entry_head then
110       @entry_head + pieces.join('')
111     else
112       pieces.join('')
113     end
114   self.entry_ended_pos = p1
115   return self.entry
116 end

gets an entry

rewind ()

Source

   # File lib/bio/appl/blast/rpsblast.rb
67 def rewind
68   @entry_head = nil
69   super
70 end

Rewinds the stream

Calls superclass method Bio::FlatFile::Splitter::Template#rewind

skip_leader ()

Source

   # File lib/bio/appl/blast/rpsblast.rb
61 def skip_leader
62   stream.skip_spaces
63   return nil
64 end

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