created find_orphans Biopiece

[biopieces.git] / bp_bin / find_orphans

diff --git a/bp_bin/find_orphans b/bp_bin/find_orphans
new file mode 100755 (executable)
index 0000000..d8f2e4e
--- /dev/null
+++ b/bp_bin/find_orphans
@@ -0,0 +1,81 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Identify paired end orphan in records with sequence data.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'pp'
+
+options = Biopieces.options_parse(ARGV)
+
+class Illumina
+  def self.name_match?(name1, name2)
+
+    if name1[-2] == '/'
+      name1[0 .. -3 ] == name2[0 .. -3]                # Solexa and Illumina <= 1.5 version names
+    else
+      name1.split(" ").first == name2.split(" ").first # Illumina > 1.5 version names
+    end
+  end
+end
+
+records = []
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    records << record
+
+    if records.size == 2
+      if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME])
+        records.first[:TYPE] = "paired"
+        records.last[:TYPE]  = "paired"
+
+        output.puts records.first
+        output.puts records.last
+
+        records = []
+      else
+        records.first[:TYPE] = "orphan"
+        output.puts records.first
+
+        records.shift
+      end
+    end
+  end
+
+  records.each do |record|
+    record[:TYPE] = "orphan"
+    output.puts record
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__