moved usearch code to external file

[biopieces.git] / code_ruby / lib / maasha / usearch.rb

diff --git a/code_ruby/lib/maasha/usearch.rb b/code_ruby/lib/maasha/usearch.rb
new file mode 100644 (file)
index 0000000..b0c8c2f
--- /dev/null
+++ b/code_ruby/lib/maasha/usearch.rb
@@ -0,0 +1,153 @@
+# Copyright (C) 2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/fasta'
+
+# Error class for all exceptions to do with Usearch.
+class UsearchError < StandardError; end
+
+SORT_LIMIT = 2_000_000_000   # use mergesort for files biggern than 2Gb.
+
+class Usearch
+  include Enumerable
+
+  def initialize(infile, outfile, options)
+    @infile  = infile
+    @outfile = outfile
+    @options = options
+    @command = []
+  end
+
+  # Method that calls Usearch sorting for sorting a FASTA file
+  # according to decending sequence length.
+  def sort_length
+    # 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 that calls Usearch sorting for sorting a FASTA file
+  # according to cluster size.
+  def sort_size
+    # usearch -sortsize seqs.fasta -output seqs.sorted.fasta
+    @command << "usearch --sortsize #{@infile} --output #{@infile}.sort"
+
+               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
+    @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
+    @command << "--rev"
+
+               execute
+  end
+
+       # Method to parse a Uclust .uc file and for each line of data
+       # yield a Biopiece record.
+  def each_cluster
+    record = {}
+
+    File.open(@outfile, mode="r") do |ios|
+      ios.each_line do |line|
+        if line !~ /^#/
+          fields = line.chomp.split("\t")
+
+          next if fields[0] == 'C'
+
+          record[:TYPE]     = fields[0]
+          record[:CLUSTER]  = fields[1].to_i
+          record[:IDENT]    = fields[3].to_f
+          record[:Q_ID]     = fields[8]
+
+          yield record
+        end
+      end
+    end
+
+    self # conventionally
+  end
+
+       # Method to parse a Useach user defined tabular file and for each line of data
+       # yield a Biopiece record.
+  def each_hit
+    record = {}
+
+    File.open(@outfile, mode="r") do |ios|
+      ios.gets   # skip comment line
+      ios.each_line do |line|
+        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
+
+    self # conventionally
+  end
+
+  private
+
+       # Method to execute a command using a system() call.
+       # The command is composed of bits from the @command variable.
+       def execute
+               @command.unshift "nice -n 19"
+    @command << "--rev" if @options[:comp]
+               @command << "> /dev/null 2>&1" unless @options[:verbose]
+               command = @command.join(" ")
+    system(command)
+    raise "Command failed: #{command}" unless $?.success?
+
+               @command = []
+       end
+end
+
+__END__
+