Class: Cassiopee::Crawler

Inherits:
Object
  • Object
show all
Defined in:
lib/cassiopee.rb

Overview

Base class to index and search through a string

Constant Summary collapse

METHOD_DIRECT = 
0
METHOD_SUFFIX = 
1
FILE_SUFFIX_EXT = 
".sfx"
FILE_SUFFIX_POS = 
".sfp"
SUFFIXLEN = 
'suffix_length'

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Crawler 



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# File 'lib/cassiopee.rb', line 299

def initialize
    @useAmbiguity = false
    @ambiguous = nil
      @useCache = false
    @file_suffix = "crawler"
      
      @method = 0
      
      @prev_min_position = 0
      @prev_max_position = 0
    
      
    @suffix = nil
    @suffixmd5 = nil
    @position = 0
    
    @suffixes = Hash.new
    
    @matches = Array.new
    @curmatch = 0
    @use_store = false
    
    @sequence = nil
      
      @comments = Array["#"]
      
      @cache = Cassiopee::CrawlerCache.new

end

Instance Attribute Details

#ambiguous ⇒ Object

Ambiguity map (Hash)



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# File 'lib/cassiopee.rb', line 264

def ambiguous
  @ambiguous
end

#comments ⇒ Object

Array of comment characters to skip lines in input sequence file



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# File 'lib/cassiopee.rb', line 258

def comments
  @comments
end

#file_suffix ⇒ Object

Suffix files name/path



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# File 'lib/cassiopee.rb', line 252

def file_suffix
  @file_suffix
end

#maxthread ⇒ Object

Max number fo threads to use (not yet used)



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# File 'lib/cassiopee.rb', line 254

def maxthread
  @maxthread
end

#method ⇒ Object

Method for search FORCE or SUFFIX

  • SUFFIX loads all suffixes and search through them afterwards, interesting for multiple searches (suffixes are reused)

  • FORCE checks matches while crossing the suffixes. Does not keep parsed data for later search FORCE method does not yet support optimal filters



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# File 'lib/cassiopee.rb', line 270

def method
  @method
end

#use_store ⇒ Object

Use persistent suffix file ?



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# File 'lib/cassiopee.rb', line 256

def use_store
  @use_store
end

#useAmbiguity ⇒ Object

Use alphabet ambiguity (dna/rna) in search, automatically set with loadAmbiguityFile



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# File 'lib/cassiopee.rb', line 250

def useAmbiguity
  @useAmbiguity
end

#useCache ⇒ Object

Manage basic cache to store previous match



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# File 'lib/cassiopee.rb', line 261

def useCache
  @useCache
end

Instance Method Details

#clear ⇒ Object

Clear suffixes in memory If using use_store, clear the store too



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# File 'lib/cassiopee.rb', line 340

def clear
  @suffixes = Hash.new
      @matches.clear
      @pattern = nil
      @prev_max_position = 0
      @prev_min_position = 0
      @cache.clearCache()
  File.delete(@file_suffix+FILE_SUFFIX_POS) unless !File.exists?(@file_suffix+FILE_SUFFIX_POS)
end

#extractSuffix(start, len) ⇒ Object

Extract un suffix from suffix file based on md5 match



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# File 'lib/cassiopee.rb', line 586

def extractSuffix(start,len)
  sequence = ''
        begin
          file = File.new(@file_suffix+FILE_SUFFIX_EXT, "r")
file.pos = start
          sequence = file.read(len)
          file.close
        rescue => err
          puts "Exception: #{err}"
          return nil
        end
  return sequence
end

#filter(posArray) ⇒ Object

Filter the array of positions with defined position filter



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# File 'lib/cassiopee.rb', line 563

def filter(posArray)
  $log.debug("filter the position with " << @min_position.to_s << " and " << @max_position.to_s)
  if(@min_position==0 && @max_position==0)
    return posArray
  end
  filteredArray = Array.new
  i = 0
  posArray.each do |pos|
    if(i==0)
      # First elt of array is match length
      filteredArray << pos
    end
    if(i>0 && pos>=@min_position && pos<=@max_position)
      filteredArray << pos
    end
    i +=1
  end
  return filteredArray
end

#filter_position(min, max) ⇒ Object

Must be called after index creation or load



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# File 'lib/cassiopee.rb', line 435

def filter_position(min,max)
    if(!use_store)
    clear()
  end
      @prev_min_position = @min_position
      @prev_max_position = @max_position
  @min_position = min
  @max_position = max
end

#filterCost ⇒ Object 



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# File 'lib/cassiopee.rb', line 333

def filterCost
  filterOptimal(1)
end

#filterLength ⇒ Object 



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# File 'lib/cassiopee.rb', line 329

def filterLength
  filterOptimal(0)
end

#indexFile(f) ⇒ Object

Index an input file Clear existing indexes



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# File 'lib/cassiopee.rb', line 359

def indexFile(f)
 # Parse file, map letters to reduced alphabet
 # Later on, use binary map instead of ascii map
 # Take all suffix, order by length, link to position map on other file
 # Store md5 for easier compare? + 20 bytes per suffix
    @sequence = readSequence(f)
    clear()
    @min_position = 0
        @max_position = 0
end

#indexString(s) ⇒ Object

Index an input string Clear existing indexes



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# File 'lib/cassiopee.rb', line 373

def indexString(s)
    @sequence = s
    File.open(@file_suffix+FILE_SUFFIX_EXT, 'w') do |data|
      data.puts(@sequence)
    end
    clear()
    @min_position = 0
        @max_position = 0
end

#loadAmbiguityFile(f) ⇒ Object

Load ambiguity rules from a file File format should be:

  • A=B,C D=E,F …



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# File 'lib/cassiopee.rb', line 390

def loadAmbiguityFile(f)
  if(!File.exists?(f))
     $log.error("File "<< f << "does not exists")
   exit(1)
  end
  @ambiguous = Hash.new
  file = File.new(f, "r")
  while (line = file.gets)
    definition = line.downcase.chomp
  ambdef = definition.split('=')
  ambequal = ambdef[1].split(',')
  @ambiguous[ambdef[0]] = ambequal
  end
  @useAmbiguity = true
  $log.debug("loaded ambiguity rules: " << @ambiguous.inspect())
  file.close

end

#loadIndex ⇒ Object

Load sequence from a previous index command



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# File 'lib/cassiopee.rb', line 411

def loadIndex
  seq = ''
  begin
    file = File.new(@file_suffix+FILE_SUFFIX_EXT, "r")
    while (line = file.gets)
      input = line.downcase.chomp
      seq << input
    end
    file.close
  rescue => err
    $log.error("Exception: #{err}")
    exit()
  end
  @sequence = seq
  clear()
          @min_position = 0
      @max_position = 0
end

#next ⇒ Object

Iterates over matches



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# File 'lib/cassiopee.rb', line 602

def next
  if(@curmatch<@matches.length)
    @curmatch = @curmatch + 1
    return @matches[@curmatch-1]
  else
    @curmatch = 0
    return nil
  end
end

#searchApproximate(s, edit) ⇒ Object 



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# File 'lib/cassiopee.rb', line 494

def searchApproximate(s,edit)
    
  if(edit==0 && !@useAmbiguity) 
    return searchExact(s)
  end
      allowederrors = edit
  if(edit>=0)
    useHamming = true
    minmatchsize = s.length
    maxmatchsize = s.length
        updateCache(1,edit)
        @matches = @cache.loadCache()
  else
    useHamming = false
    edit = edit * (-1)
      minmatchsize = s.length - edit
      maxmatchsize = s.length + edit
        updateCache(2,edit)
        @matches = @cache.loadCache()
    end
      
      if(@matches.length>0)
        return @matches
      end
      
      s = s.downcase
    
      
    #@matches.clear
      @pattern = Digest::MD5.hexdigest(s)
      
      parseSuffixes(@sequence,minmatchsize,maxmatchsize,allowederrors,s)
    
      return cache?(@matches) unless(method == METHOD_SUFFIX)
      
 
    
         
  @suffixes.each do |md5val,posArray|
    if(md5val == SUFFIXLEN)
      next
    end
    if (md5val == @pattern)
      filteredPosArray = filter(posArray)
            match = Array[md5val, 0, filteredPosArray]
$log.debug "Match: " << match.inspect
@matches << match
          else
if(posArray[0]>= minmatchsize && posArray[0] <= maxmatchsize)
  # Get string
  seq = extractSuffix(posArray[1],posArray[0])
            errors = isApproximateEqual?(seq,s,useHamming,edit)
            
  if(errors>=0)
    filteredPosArray = filter(posArray)
      match = Array[md5val, errors, filteredPosArray]
    $log.debug "Match: " << match.inspect
    @matches << match
  end
end
        end
  
  end
  
  return cache?(@matches) 
end

#searchExact(s) ⇒ Object

Search exact match



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# File 'lib/cassiopee.rb', line 447

def searchExact(s)
    
    if(@useAmbiguity)
      return searchApproximate(s,0)
    end
    
s = s.downcase

    updateCache(0,0)
    @matches = @cache.loadCache()
    
    if(@matches.length>0)
      return cache?(@matches)
    end
    
    #@matches.clear
    
    @pattern = Digest::MD5.hexdigest(s)
    
    parseSuffixes(@sequence,s.length,s.length,0,s)

    return @matches unless(method == METHOD_SUFFIX)
    
 # Search required length, compare (compare md5?)
 # MD5 = 128 bits, easier to compare for large strings
    
      
      matchsize = @pattern.length
      
    @suffixes.each do |md5val,posArray|
        if (isMatchEqual?(md5val))
            match = Array[md5val, 0, posArray]
$log.debug "Match: " << match.inspect
@matches << match
        end
    end
return cache?(@matches) 

end

#setLogLevel(level) ⇒ Object

Set Logger level



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# File 'lib/cassiopee.rb', line 352

def setLogLevel(level)
    $log.level = level
end

#to_pos ⇒ Object 



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# File 'lib/cassiopee.rb', line 612

def to_pos
  positions = Hash.new
  @matches.each do |match|
    # match = Array[md5val, errors, posArray]
    i=0
        len = 0
    match[2].each do |pos|
      if(i==0)
        len = pos
      else
        if(positions.has_key?(pos))
         posmatch = positions[pos]
         posmatch << Array[len,match[1]]

        
        else
          posmatch = Array.new
          posmatch << Array[len,match[1]]
          positions[pos] = posmatch
        end
      end
      i += 1
    end
   
  end
    return positions.sort
end

#to_s ⇒ Object 



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# File 'lib/cassiopee.rb', line 640

def to_s
  puts '{ matches: "' << @matches.length << '" }'
end