require 'maasha/biopieces'
require 'maasha/fasta'
-
-SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
-
-class Uclust
- 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
- # 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 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.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
-
- 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
+require 'maasha/usearch'
casts = []
casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
input.each_record do |record|
output.puts record
- if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+ if record[:SEQ_NAME] and record[:SEQ]
fasta_io.puts Seq.new_bp(record).to_fasta
end
end
end
end
-uc = Uclust.new(file_fasta, file_uclust, options)
-uc.sort unless options[:no_sort]
-uc.cluster
+us = Usearch.new(file_fasta, file_uclust, options)
+us.sort_length unless options[:no_sort]
+us.cluster
hash = {}
-uc.each do |record|
+us.each_cluster do |record|
hash[record[:Q_ID].to_sym] = record.dup
end
Biopieces.open(file_records, options[:stream_out]) do |input, output|
input.each_record do |record|
- if record.has_key? :SEQ_NAME and record.has_key? :SEQ
- if hash.has_key? record[:SEQ_NAME].to_sym
- uc = hash[record[:SEQ_NAME].to_sym]
- record[:CLUSTER] = uc[:CLUSTER].to_i
- record[:IDENT] = uc[:IDENT].to_i
- record[:IDENT] = '*' if uc[:TYPE] == 'S'
+ if record[:SEQ_NAME] and record[:SEQ]
+ if hash[record[:SEQ_NAME].to_sym]
+ us = hash[record[:SEQ_NAME].to_sym]
+ record[:CLUSTER] = us[:CLUSTER].to_i
+ record[:IDENT] = us[:IDENT].to_i
+ record[:IDENT] = '*' if us[:TYPE] == 'S'
end
end