removing patscan ruby crap

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1150 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/patfind.rb b/code_ruby/Maasha/lib/patfind.rb
deleted file mode 100644 (file)
index 1696b62..0000000
--- a/code_ruby/Maasha/lib/patfind.rb
+++ /dev/null
@@ -1,48 +0,0 @@
-DEBUG = false
-
-module PatFind
-  @@pos = 0
-
-  def scan(pattern, max_mis = 0, max_ins = 0, max_del = 0)
-    if block_given?
-      while m = match(pattern, @@pos, max_mis, max_ins, max_del)
-        @@pos += m.pos + 1
-
-        yield m
-      end
-    else
-      matches = []
-
-      while m = match(pattern, @@pos, max_mis, max_ins, max_del)
-        matches << m
-
-        @@pos += m.pos + 1
-      end
-
-      return matches
-    end
-  end
-
-  def match(pattern, pos = 0, max_mis = 0, max_ins = 0, max_del = 0)
-    if pattern[0] == self.seq[pos]
-      puts self.seq[pos]
-    end
-
-    block_given? ? (yield m) : (return m)
-  end
-end
-
-# Class containing match information for use with PatFind.
-class Match
-  attr_accessor :pattern, :pos, :length, :mismatches, :insertions, :deletions
-
-  def initialize(pattern, pos, mismatches, insertions, deletions)
-    @pattern    = pattern
-    @pos        = pos
-    @length     = pattern.length
-    @mismatches = mismatches
-    @insertions = insertions
-    @deletions  = deletions
-  end
-end
-

diff --git a/code_ruby/Maasha/lib/patscan.rb b/code_ruby/Maasha/lib/patscan.rb
deleted file mode 100644 (file)
index 2d64773..0000000
--- a/code_ruby/Maasha/lib/patscan.rb
+++ /dev/null
@@ -1,142 +0,0 @@
-require 'fasta'
-require 'open3'
-require 'tempfile'
-
-# Error class for all exceptions to do with Patscan.
-class PatscanError < StandardError; end
-
-# Class for executing the commandline tool scan_for_matches, which is used like this:
-# scan_for_matches [options] pattern_file < fasta_data > output_data
-class Patscan
-  @@initialized = false
-  @@options     = []
-
-  # Method to initialize a Patscan object and where we save the pattern file
-  # and format the options only once.
-  def initialize(pattern, args = {})
-    unless @@initialized
-      check_args(args)
-      pattern_save(pattern)
-      @@initialized = true
-    end
-  end
-
-  # Method to scan the sequence in a Seq object for a pattern specified
-  # during initialization.
-  def scan(seq)
-    begin
-      stdin, stdout, stderr, wait_thr = Open3.popen3("scan_for_matches #{@@options.join(" ")}" )
-
-      stdin.puts seq.to_fasta
-
-      stdin.close
-
-      exit_status = wait_thr.value
-
-      raise PatscanError, "scan_for_matches failed: #{stderr.read}" unless exit_status.success?
-
-      fasta = Fasta.new(stdout)
-
-      fasta.each do |entry|
-        yield Match.new(entry)
-      end
-    ensure
-      stdin.close unless stdin.closed?
-      stdout.close
-      stderr.close
-    end
-  end
-
-  private
-
-  # Method to check arguments to patscan and add these to @@options.
-  def check_args(args)
-    args.each_pair do |key,val|
-      case key
-      when "complement".to_sym
-        raise PatscanError, "Bad patscan complement value: #{val}" unless val == true or val == false
-        @@options << "-c" if val == true
-      when "protein".to_sym
-        raise PatscanError, "Bad patscan protein value: #{val}" unless val == true or val == false
-        @@options << "-p" if val == true
-      when "max_hits".to_sym
-        raise PatscanError, "Bad patscan protein value: #{val}" unless val.is_a? Fixnum and val > 0
-        @@options << "-m #{val}"
-      else
-        raise PatscanError, "Unknown argument: #{key}"
-      end
-    end
-  end
-
-  # Method to save pattern file and add
-  # the path to @@options.
-  def pattern_save(pattern)
-    file = Tempfile.new("patscan.pat")
-    ios  = File.open(file, mode="w")
-    ios << pattern
-    ios.close
-
-    @@options << file.path
-  end
-end
-
-# Error class for all exceptions to do with Match.
-class MatchError < StandardError; end
-
-# Class for matches from scan_for_matches.
-class Match
-  attr_accessor :pattern, :pat_beg, :pat_end, :strand
-  # Method to initialize a Match object from
-  # a scan_for_matches hit given as a Seq object.
-  def initialize(entry)
-    @pattern           = pattern_get(entry)
-    @pat_beg, @pat_end = pattern_beg_end(entry)
-    @strand            = pattern_strand
-  end
-
-  def to_bp
-    record = {}
-    record[:PATTERN]  = self.pattern
-    record[:PAT_BEG]  = self.pat_beg
-    record[:PAT_END]  = self.pat_end
-    record[:PAT_LEN]  = self.pat_end - self.pat_beg + 1
-    record[:STRAND]   = self.strand
-    record
-  end
-
-  private
-
-  # Method to extract the pattern.
-  def pattern_get(entry)
-    entry.seq
-  end
-
-  # Method to extract the begin and end coordinates of
-  # the match. Note that scan_for_matches output is 1-based.
-  def pattern_beg_end(entry)
-    if entry.seq_name =~ /\[(\d+),(\d+)\]$/
-      pat_beg = $1.to_i - 1
-      pat_end = $2.to_i - 1
-    else
-      raise MatchError, "Failed to get begin and end from: #{entry.seq_name}"
-    end
-
-    [pat_beg, pat_end]
-  end
-
-  # Method to determine the strand of the match - and reverse
-  # the pattern begin and end coordinates if the match is on the
-  # minus strand.
-  def pattern_strand
-    if @pat_beg < @pat_end
-      strand = "+"
-    else
-      strand = "-"
-
-      @pat_beg, @pat_end = @pat_end, @pat_beg
-    end
-
-    strand
-  end
-end
-

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 29132370f97dc84bf66678a29a5eae056010dec6..4c2829225e8817e9c139288d6943b3976cf9163d 100644 (file)
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -1,5 +1,3 @@
-require 'patscan'
-require 'patfind'
 
 # Residue alphabets
 DNA     = %w[a t c g]
@@ -15,8 +13,6 @@ SCORE_ILLUMINA = 64
 class SeqError < StandardError; end
 
 class Seq
-  include PatFind
-
   attr_accessor :seq_name, :seq, :type, :qual
 
   # Initialize a sequence object with the following arguments:
@@ -197,15 +193,6 @@ class Seq
     end
   end
 
-  # Method that invoces patscan (a.k.a scan_for_matches) on
-  # a sequence object.
-  def patscan(pattern, args = {})
-    ps = Patscan.new(pattern, args)
-    ps.scan(self) do |match|
-      yield match
-    end
-  end
-
   private
 
   # Method to convert a Solexa score (odd ratio) to