#!/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
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
require 'maasha/biopieces'
require 'maasha/fasta'
+SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
+
class Uclust
include Enumerable
@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
- @command << "uclust --sort #{@infile} --output #{@infile}.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
- # uclust --ublast query_seqs.fasta --db database.fasta --blast6out filename --evalue E
- @options[:e_val] = 10 unless @options[:e_val]
- @command << "uclust --ublast #{@infile} --db #{@options[:database]} --blast6out #{@outfile} --evalue #{@options[:e_val]}"
-
- execute
- end
-
# Method to execute database search.
def usearch
- # uclust --query query.fasta --db db.fasta --uc results.uc --id 0.90 [--evalue E]
- @command << "uclust --query #{@infile} --db #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
+ # 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
# Method to execute clustering de novo.
- def uclust
- # uclust --input seqs_sorted.fasta --uc results.uc --id 0.90
- @command << "uclust --input #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
+ def cluster
+ @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
execute
end
# Method to execute clustering to database plus de novo if not matched.
def usearch_uclust
- # uclust --input seqs_sorted.fasta --lib db.fasta --uc results.uc --id 0.90
- @command << "uclust --input #{@infile} --lib #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
- @command << "--lib #{@options[:database]}" if @options.has_key? :database
+ # 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
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]
end
end
-ok_methods = "ublast,usearch,uclust,usearch_uclust"
+ok_methods = "usearch,uclust,usearch_uclust"
casts = []
casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
Fasta.open(infile, mode="w") do |fasta_io|
input.each_record do |record|
output.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
uclust.sort unless options[:no_sort]
case options[:method].to_s
- when "ublast" then uclust.ublast
when "usearch" then uclust.usearch
- when "uclust" then uclust.uclust
+ when "uclust" then uclust.cluster
when "usearch_uclust" then uclust.usearch_uclust
else raise "Unknown method: #{options[:method]}"
end