#!/usr/bin/env ruby
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2011 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
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-#
+# Run Uclust on sequences in the stream.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+require 'maasha/biopieces'
+require 'maasha/fasta'
-require 'biopieces'
-require 'fasta'
+SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
class Uclust
include Enumerable
- def initialize(infile, outfile)
+ def initialize(infile, outfile, options)
@infile = infile
@outfile = outfile
+ @options = options
+ @command = []
end
- # Method that calls Uclusts sorting for sorting a FASTA file
+ # Method that calls Usearch sorting for sorting a FASTA file
# according to decending sequence length.
- def sort(options)
- command = "nice -n 19"
- command << " uclust --sort #{@infile} --output #{@infile}.sort"
- command << " > /dev/null 2>&1" unless options[:verbose]
- system(command)
- raise "Failed sorting file: #{@infile}" unless $?.success?
+ 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
- def ublast(options)
- # uclust --ublast query_seqs.fasta --db database.fasta --blast6out filename --evalue E
- options[:e_val] = 10 if options[:e_val].is_nil?
- command = "nice -n 19"
- command << " uclust --ublast #{@infile} --db #{options[:database]} --uc #{@outfile} --evalue #{options[:e_val]}"
- command << " > /dev/null 2>&1" unless options[:verbose]
- system(command)
- raise "Command failed: #{command}" unless $?.success?
- end
+ # Method to execute clustering de novo.
+ def cluster
+ @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
- def usearch(options)
- # uclust --query query.fasta --db db.fasta --uc results.uc --id 0.90 [--evalue E]
- command = "nice -n 19"
- command << " uclust --query #{@infile} --db #{options[:database]} --uc #{@outfile} --id #{options[:identity]}"
- command << " --evalue #{options[:e_val]}" if options.has_key? :e_val
- command << " > /dev/null 2>&1" unless options[:verbose]
- system(command)
- raise "Command failed: #{command}" unless $?.success?
+ execute
end
- def uclust(options)
- # uclust --input seqs_sorted.fasta --uc results.uc --id 0.90
- command = "nice -n 19"
- command << " uclust --input #{@infile} --uc #{@outfile} --id #{options[:identity]}"
- command << " > /dev/null 2>&1" unless options[:verbose]
- system(command)
- raise "Command failed: #{command}" unless $?.success?
+ # 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 << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
+
+ execute
end
- def usearch_uclust(options)
- # uclust --input seqs_sorted.fasta --lib db.fasta --uc results.uc --id 0.90
- command = "nice -n 19"
- command << " uclust --input #{@infile} --lib #{options[:database]} --uc #{@outfile} --id #{options[:identity]}"
- command << " --lib #{options[:database]}" if options.has_key? :database
- command << " > /dev/null 2>&1" unless options[:verbose]
- system(command)
- raise "Command failed: #{command}" unless $?.success?
+ # 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
+ # yield a Biopiece record.
def each
record = {}
File.open(@outfile, mode="r") do |ios|
ios.each_line do |line|
if line !~ /^#/
- fields = line.split("\t")
+ fields = line.chomp.split("\t")
record[:REC_TYPE] = "UCLUST"
record[:TYPE] = fields[0]
- record[:CLUSTER] = fields[1]
- record[:SEQ_LEN] = fields[2]
- record[:IDENT] = fields[3]
+ 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]
- record[:S_BEG] = fields[6]
+ 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]
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
-ok_methods = "ublast,usearch,uclust,usearch_uclust"
+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}
-bp = Biopieces.new
+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.
-options = bp.parse(ARGV, casts)
+tmpdir = Biopieces.mktmpdir
+infile = File.join(tmpdir, "in.fna")
+outfile = File.join(tmpdir, "out.uc")
-tmpdir = bp.mktmpdir
-infile = "#{tmpdir}/in.fna"
-outfile = "#{tmpdir}/out.uc"
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ Fasta.open(infile, mode="w") do |fasta_io|
+ input.each_record do |record|
+ output.puts record
-Fasta.open(infile, mode="w") do |fasta_io|
- bp.each_record do |record|
- bp.puts record
- fasta_io.puts record
+ if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+ fasta_io.puts Seq.new_bp(record).to_fasta
+ end
+ end
end
-end
-uclust = Uclust.new(infile, outfile)
-uclust.sort(options) unless options[:no_sort]
+ uclust = Uclust.new(infile, outfile, options)
+ uclust.sort unless options[:no_sort] or options[:method] == "usearch"
-case options[:method].to_s
-when "ublast" then uclust.ublast(options)
-when "usearch" then uclust.usearch(options)
-when "uclust" then uclust.uclust(options)
-when "usearch_uclust" then uclust.usearch_uclust(options)
-else raise "Unknown method: #{options[:method]}"
-end
+ case options[:method].to_s
+ when "uclust" then uclust.cluster
+ when "usearch" then uclust.usearch
+ when "usearch_uclust" then uclust.usearch_uclust
+ end
-uclust.each do |record|
- bp.puts record
+ uclust.each do |record|
+ output.puts record
+ end
end
projects / biopieces.git / blobdiff