3 # Copyright (C) 2007-2011 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
21 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
23 # This program is part of the Biopieces framework (www.biopieces.org).
25 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
27 # Run Uclust on sequences in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
32 require 'maasha/fasta'
33 require 'maasha/usearch'
36 casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
37 casts << {:long=>'comp', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 casts << {:long=>'identity', :short=>'i', :type=>'float', :mandatory=>true, :default=>0.9, :allowed=>nil, :disallowed=>nil}
40 options = Biopieces.options_parse(ARGV, casts)
42 tmpdir = Biopieces.mktmpdir
43 file_records = File.join(tmpdir, "data.stream")
44 file_fasta = File.join(tmpdir, "in.fna")
45 file_uclust = File.join(tmpdir, "out.uc")
47 Biopieces.open(options[:stream_in], file_records) do |input, output|
48 Fasta.open(file_fasta, mode="w") do |fasta_io|
49 input.each_record do |record|
52 if record.has_key? :SEQ_NAME and record.has_key? :SEQ
53 fasta_io.puts Seq.new_bp(record).to_fasta
59 us = Usearch.new(file_fasta, file_uclust, options)
60 us.sort_length unless options[:no_sort]
65 us.each_cluster do |record|
66 hash[record[:Q_ID].to_sym] = record.dup
69 Biopieces.open(file_records, options[:stream_out]) do |input, output|
70 input.each_record do |record|
71 if record.has_key? :SEQ_NAME and record.has_key? :SEQ
72 if hash.has_key? record[:SEQ_NAME].to_sym
73 us = hash[record[:SEQ_NAME].to_sym]
74 record[:CLUSTER] = us[:CLUSTER].to_i
75 record[:IDENT] = us[:IDENT].to_i
76 record[:IDENT] = '*' if us[:TYPE] == 'S'
85 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<