From 773dcafe5d5199784cbbb44eff03d3fe10a13cb0 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 21 Jan 2013 13:37:11 +0000
Subject: [PATCH] added assemble_pairs biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2081 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/assemble_pairs | 117 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 117 insertions(+)
 create mode 100755 bp_bin/assemble_pairs

diff --git a/bp_bin/assemble_pairs b/bp_bin/assemble_pairs
new file mode 100755
index 0000000..440810b
--- /dev/null
+++ b/bp_bin/assemble_pairs
@@ -0,0 +1,117 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2013 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Assemble ordered overlapping pair-end sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/fastq'
+require 'pp'
+
+casts = []
+casts << {:long=>'overlap', :short=>'o', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+tmpdir   = Biopieces.mktmpdir
+file_in1 = File.join(tmpdir, "in1.fq")
+file_in2 = File.join(tmpdir, "in2.fq")
+file_out = File.join(tmpdir, "out.fq")
+
+io_in1 = Fastq.open(file_in1, 'w')
+io_in2 = Fastq.open(file_in2, 'w')
+
+name1  = ""
+name2  = ""
+entry1 = ""
+entry2 = ""
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
+      entry = Seq.new_bp(record)
+
+      case entry.seq_name
+      when /^(.+)\/(\d)$/   # Illumina 1.5
+        name = $1
+        pair = $2.to_i
+        type = 15
+      when /^(.+) (\d):/    # Illumina 1.8
+        name = $1
+        pair = $2.to_i
+        type = 18
+      else
+        $stderr.puts "WARNING: Unmatched sequence name: #{entry.seq_name}"
+      end
+
+      if pair == 1
+        name1  = name.dup
+        entry1 = entry.dup
+      else
+        name2  = name.dup
+        entry2 = entry.dup
+      end
+
+      if name1 != nil and name1 == name2
+        io_in1.puts entry1.to_fastq
+        io_in2.puts entry2.to_fastq
+      end
+    end
+  end
+
+  io_in1.close
+  io_in2.close
+
+  cmd = "pandaseq"
+  cmd << " -6"
+  cmd << " -F"
+  cmd << " -B"
+  cmd << " -N"
+  cmd << " -o #{options[:overlap]}"
+  cmd << " -f #{file_in1}"
+  cmd << " -r #{file_in2}"
+  cmd << " > #{file_out}"
+  cmd << " 2> /dev/null" unless options[:verbose]
+
+  $stderr.puts cmd if options[:verbose]
+
+  system(cmd)
+
+  raise RunTimeError "Error: command failed: #{cmd}" unless $?.success?
+
+  Fastq.open(file_out) do |ios|
+    ios.each do |entry|
+      output.puts entry.convert_scores!('illumina18', 'illumina15').to_bp
+    end
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-- 
2.39.2