require 'maasha/biopieces'
require 'maasha/fasta'
-
-class Usearch
- include Enumerable
-
- def initialize(infile, outfile, options)
- @infile = infile
- @outfile = outfile
- @options = options
- @command = []
- 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
-
- execute
- end
-
- # 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|
- 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"
- @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=>'database', :short=>'d', :type=>'file!', :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}
+casts << {long: 'program', short: 'p', type: 'string', mandatory: false, default: 'global', allowed: "local,global", disallowed: nil}
+casts << {long: 'database', short: 'd', type: 'file!', mandatory: true, 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}
+casts << {long: 'cpus', short: 'c', type: 'uint', mandatory: false, default: 1, allowed: nil, disallowed: "0"}
+casts << {long: 'maxaccepts', short: 'm', type: 'uint', mandatory: false, default: 0, allowed: nil, disallowed: nil}
options = Biopieces.options_parse(ARGV, casts)
-raise ArgumentError, "--identity or --e_val must be specified" unless options[:identity] or options[:e_val]
+if options[:program] == 'global'
+ raise ArgumentError, "--identity be specified for global search" unless options[:identity]
+ raise ArgumentError, "--e_val is invalid for global search" if options[:e_val]
+else
+ raise ArgumentError, "--identity or --e_val must be specified" unless options[:identity] or options[:e_val]
+end
tmpdir = Biopieces.mktmpdir
infile = File.join(tmpdir, "in.fna")
outfile = File.join(tmpdir, "out.uc")
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- Fasta.open(infile, mode="w") do |fasta_io|
+ Fasta.open(infile, "w") do |fasta_io|
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
- uc = Usearch.new(infile, outfile, options)
+ us = Usearch.new(infile, outfile, options)
- uc.usearch
+ case options[:program]
+ when "local" then us.usearch_local
+ when "global" then us.usearch_global
+ else raise "no such program #{options[:program]}"
+ end
- uc.each do |record|
+ us.each_hit do |record|
output.puts record
end
end