added denoise_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1743 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/denoise_seq b/bp_bin/denoise_seq
new file mode 100755 (executable)
index 0000000..ff557b4
--- /dev/null
+++ b/bp_bin/denoise_seq
@@ -0,0 +1,120 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2012 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
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Denoises sequences with quality scores in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'pp'
+require 'maasha/biopieces'
+require 'maasha/seq'
+require 'maasha/fastq'
+require 'maasha/fasta'
+require 'maasha/align'
+require 'maasha/usearch'
+
+casts = []
+casts << {:long=>'identity',    :short=>'i', :type=>'float', :mandatory=>true, :default=>0.97, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cluster_min', :short=>'c', :type=>'uint',  :mandatory=>true, :default=>2,    :allowed=>nil, :disallowed=>"0"}
+
+options          = Biopieces.options_parse(ARGV, casts)
+tmpdir           = Biopieces.mktmpdir
+fastq_file       = File.join(tmpdir, "test.fq")
+fasta_file       = File.join(tmpdir, "test.fna")
+fasta_file_align = File.join(tmpdir, "test.aln.fna")
+
+def alignment_to_fastq(entries, index)
+  entries.each do |entry|
+    cluster, ident, name = entry.seq_name.split('|')
+
+    entry.qual = index.get(name).qual # disk based lookup
+
+    entry.seq.scan(/-+/) do |m|
+      entry.qual = entry.qual[0 ... $`.length] + ('@' * m.length) + entry.qual[$`.length .. -1]
+    end
+  end
+end
+
+index     = FastqIndex.new
+seq_count = 0
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  Fasta.open(fasta_file, "w") do |fasta_io|
+    Fastq.open(fastq_file, "w") do |fastq_io|
+      input.each_record do |record|
+        if record.has_key? :SEQ and record.has_key? :SCORES
+          entry = Seq.new_bp(record)
+          entry.seq_name = seq_count.to_s
+
+          fasta_io.puts entry.to_fasta
+          fastq_io.puts entry.to_fastq
+
+          index.add(entry)
+
+          seq_count += 1
+        else
+          output.puts record
+        end
+      end
+    end
+  end
+
+  fastq_io  = File.open(fastq_file, "r")
+  index.ios = fastq_io
+
+  tot_clusters = 0
+  tot_entries  = 0
+
+  uc = Usearch.new(fasta_file, fasta_file_align, options)
+  uc.sort_length
+  uc.cluster
+  uc.ustar
+
+  uc.each_alignment do |align|
+    if align.members >= options[:cluster_min]
+      alignment_to_fastq(align.entries, index)
+
+      cons          = align.consensus
+      cons.seq_name = "#{tot_clusters}_#{align.members}"
+      cons.indels_remove
+
+      new_record = cons.to_bp
+      new_record[:CLUSTER]       = tot_clusters
+      new_record[:CLUSTER_COUNT] = align.members
+
+      puts align if options[:verbose]
+
+      output.puts new_record
+
+      tot_clusters += 1
+    end
+  end
+end
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__