From 6dce31d9c50a6e0565f816547c86009486ebf2ef Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 18 Apr 2012 08:10:47 +0000
Subject: [PATCH] added findsim_seq biopieces

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1799 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/findsim_seq | 74 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100755 bp_bin/findsim_seq

diff --git a/bp_bin/findsim_seq b/bp_bin/findsim_seq
new file mode 100755
index 0000000..d6879cc
--- /dev/null
+++ b/bp_bin/findsim_seq
@@ -0,0 +1,74 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Find similar sequences between query sequences from the stream and a database.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'pp'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/findsim'
+
+casts = []
+casts << {:long=>'database',      :short=>'d', :type=>'file!', :mandatory=>true,  :default=>nil, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'kmer',          :short=>'k', :type=>'uint',  :mandatory=>false, :default=>8,   :allowed=>"4,5,6,7,8,9", :disallowed=>nil}
+casts << {:long=>'step',          :short=>'s', :type=>'uint',  :mandatory=>false, :default=>1,   :allowed=>nil,           :disallowed=>"0"}
+casts << {:long=>'report_scores', :short=>'r', :type=>'uint',  :mandatory=>false, :default=>7,   :allowed=>nil,           :disallowed=>"0"}
+casts << {:long=>'min_score',     :short=>'m', :type=>'float', :mandatory=>false, :default=>0.5, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'query_ids',     :short=>'Q', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'subject_ids',   :short=>'S', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
+
+options    = Biopieces.options_parse(ARGV, casts)
+tmpdir     = Biopieces.mktmpdir
+query_file = File.join(tmpdir, "query.fna")
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  Fasta.open(query_file, "w") do |fasta_io|
+    input.each_record do |record|
+      if record[:SEQ_NAME] and record[:SEQ]
+        entry = Seq.new_bp(record)
+
+        fasta_io.puts entry.to_fasta
+      end
+
+      output.puts record
+    end
+  end
+
+  fs = FindSim.new(options)
+  fs.load_query(query_file)
+  fs.search_db(options[:database])
+
+  fs.each do |hit|
+    output.puts hit.to_bp
+  end
+end
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-- 
2.39.5