upgraded usearch_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1671 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/usearch_seq b/bp_bin/usearch_seq
index b20a29c672673ce690870e7f1e31d54df24e30b0..5cac9497b637fc95a1d9c4e6fd7d8e68fe9da2ba 100755 (executable)
--- a/bp_bin/usearch_seq
+++ b/bp_bin/usearch_seq
@@ -24,16 +24,14 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Run Uclust on sequences in the stream.
+# Usearch sequences in the stream against a specified database.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/biopieces'
 require 'maasha/fasta'
 
-SORT_LIMIT = 2_000_000_000   # use mergesort for files biggern than 2Gb.
-
-class Uclust
+class Usearch
   include Enumerable
 
   def initialize(infile, outfile, options)
@@ -43,70 +41,35 @@ class Uclust
     @command = []
   end
 
-  # Method that calls Usearch sorting for sorting a FASTA file
-  # according to decending sequence length.
-  def sort
-    # usearch -sort seqs.fasta -output seqs.sorted.fasta
-    if File.size(@infile) < SORT_LIMIT
-      @command << "usearch --sort #{@infile} --output #{@infile}.sort"
-    else
-      @command << "usearch --mergesort #{@infile} --output #{@infile}.sort"
-    end
-
-               execute
-
-    File.rename "#{@infile}.sort", @infile
-  end
-
-       # Method to execute clustering de novo.
-  def cluster
-    @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
-
-               execute
-  end
-
   # Method to execute database search.
   def usearch
-    # usearch --query query.fasta --db db.fasta --uc results.uc --id 0.90 [--evalue E]
-    @command << "usearch --query #{@infile} --db #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
+    @command << "usearch --query #{@infile} --db #{@options[:database]} --userout #{@outfile}"
+    @command << "--userfields target+tloz+thiz+query+bits+strand"
+    @command << "--id #{@options[:identity]}"  if @options.has_key? :identity
     @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
 
                execute
   end
 
-       # Method to execute clustering to database plus de novo if not matched.
-  def usearch_uclust
-    # usearch --cluster seqs_sorted.fasta --db db.fasta --uc results.uc --id 0.90
-    @command << "usearch --cluster #{@infile} --db #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
-
-               execute
-  end
-
-       # Method to parse a Uclust .uc file and for each line of data
+       # Method to parse a Useach .uc file and for each line of data
        # yield a Biopiece record.
   def each
     record = {}
 
     File.open(@outfile, mode="r") do |ios|
+      ios.gets   # skip comment line
       ios.each_line do |line|
-        if line !~ /^#/
-          fields = line.chomp.split("\t")
-
-          record[:REC_TYPE] = "UCLUST"
-          record[:TYPE]     = fields[0]
-          record[:CLUSTER]  = fields[1].to_i
-          record[:SEQ_LEN]  = fields[2].to_i
-          record[:IDENT]    = fields[3].to_f
-          record[:STRAND]   = fields[4]
-          record[:Q_BEG]    = fields[5].to_i
-          record[:S_BEG]    = fields[6].to_i
-          record[:S_END]    = fields[6].to_i + fields[2].to_i
-          record[:CIGAR]    = fields[7]
-          record[:Q_ID]     = fields[8]
-          record[:S_ID]     = fields[9]
-
-          yield record
-        end
+        fields = line.chomp.split("\t")
+
+        record[:REC_TYPE] = "USEARCH"
+        record[:S_ID]     = fields[0]
+        record[:S_BEG]    = fields[1].to_i
+        record[:S_END]    = fields[2].to_i
+        record[:Q_ID]     = fields[3]
+        record[:SCORE]    = fields[4].to_f
+        record[:STRAND]   = fields[5]
+
+        yield record
       end
     end
 
@@ -129,21 +92,15 @@ class Uclust
        end
 end
 
-ok_methods = "uclust,usearch,usearch_uclust"
-
 casts = []
-casts << {:long=>'no_sort',  :short=>'n', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
-casts << {:long=>'method',   :short=>'m', :type=>'string', :mandatory=>true,  :default=>"uclust", :allowed=>ok_methods, :disallowed=>nil}
-casts << {:long=>'database', :short=>'d', :type=>'file!',  :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
-casts << {:long=>'comp',     :short=>'c', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
-casts << {:long=>'identity', :short=>'i', :type=>'float',  :mandatory=>true,  :default=>0.9,      :allowed=>nil,        :disallowed=>nil}
-casts << {:long=>'e_val',    :short=>'e', :type=>'float',  :mandatory=>false, :default=>nil,      :allowed=>nil,        :disallowed=>nil}
+casts << {:long=>'database', :short=>'d', :type=>'file!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'comp',     :short=>'c', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'identity', :short=>'i', :type=>'float', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'e_val',    :short=>'e', :type=>'float', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 
-# At high identities, around 96% and above, compressed indexes are often more sensitive, faster 
-# and use less RAM. Compressed indexes are disabled by default, so I generally recommend that 
-# you specify the --slots and --w options when clustering at high identities.
+raise ArgumentError, "--identity or --e_val must be specified" unless options[:identity] or options[:e_val]
 
 tmpdir  = Biopieces.mktmpdir
 infile  = File.join(tmpdir, "in.fna")
@@ -160,16 +117,11 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     end
   end
 
-  uclust = Uclust.new(infile, outfile, options)
-  uclust.sort unless options[:no_sort] or options[:method] == "usearch"
+  uc = Usearch.new(infile, outfile, options)
 
-  case options[:method].to_s
-  when "uclust"         then uclust.cluster
-  when "usearch"        then uclust.usearch
-  when "usearch_uclust" then uclust.usearch_uclust
-  end
+  uc.usearch
 
-  uclust.each do |record|
+  uc.each do |record|
     output.puts record
   end
 end