added order_pairs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1436 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/order_pairs b/bp_bin/order_pairs
new file mode 100755 (executable)
index 0000000..8746548
--- /dev/null
+++ b/bp_bin/order_pairs
@@ -0,0 +1,80 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Order records so SEQ_NAME/1 and SEQ_NAME/2 are in the order.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/biopieces'
+require 'pp'
+
+options = Biopieces.options_parse(ARGV)
+
+hash1 = {}
+hash2 = {}
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:SEQ_NAME]
+      name = record[:SEQ_NAME][0 ... -2].to_sym
+      pair = record[:SEQ_NAME][-1].to_i
+
+      if pair == 1
+        if hash2.has_key? name
+          output.puts record
+          output.puts hash2[name]
+
+          hash2.delete(name)
+        else
+          hash1[name] = record
+        end
+      elsif pair == 2
+        if hash1.has_key? name
+          output.puts hash1[name]
+          output.puts record
+
+          hash1.delete(name)
+        else
+          hash2[name] = record
+        end
+      else
+        $stderr.puts "WARNING: Badly formatted name: #{record[:SEQ_NAME]}" if options[:verbose]
+      end
+    end
+  end
+end
+
+if options[:verbose]
+  $stderr.puts "Unmatched names with /1: #{hash1.size}"
+  $stderr.puts "Unmatched names with /2: #{hash2.size}"
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_test/in/order_pairs.in b/bp_test/in/order_pairs.in
new file mode 100644 (file)
index 0000000..3e30de4
--- /dev/null
+++ b/bp_test/in/order_pairs.in
@@ -0,0 +1,40 @@
+SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB
+SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NNNNNGNNNNNNNTANACNNNNTNNNNNNNANNNNGNNNNNCNNNNNGNN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NNNNNNNNGGNNCNANNANNNNGTNNNTNGNANNNNCNNANTTGNNNNNN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1041:14486#TTAGGC/2
+---
+SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB
+SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1
+---
+SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2
+---
+SCORES: ffffcfffffded^eddddddbdcdeedcefecfefdffecabccBB`b`
+SEQ: CCNAGGAGGAGNCAATAAGAGACCATTCGTATATGATCTCTCAGGAGAGC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1044:7943#TTAGGC/1
+---
+SCORES: ceceeee\e``cd^^Yb`b`cc``c\accccZT`YTbYb`Y\VZYBBa\Y
+SEQ: GCCGAGTAGCGTTCNTGGNTACCTTCCGATCCGCGGCCCGCCCCCTGTCT
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: AANAANANCTNCNNANCGNCGGTTTCGTNANNANNGGTTCGCANCGNNNC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2
+---

diff --git a/bp_test/out/order_pairs.out.1 b/bp_test/out/order_pairs.out.1
new file mode 100644 (file)
index 0000000..b0906df
--- /dev/null
+++ b/bp_test/out/order_pairs.out.1
@@ -0,0 +1,30 @@
+SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB
+SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NNNNNGNNNNNNNTANACNNNNTNNNNNNNANNNNGNNNNNCNNNNNGNN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2
+---
+SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB
+SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1
+---
+SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2
+---
+SCORES: ceceeee\e``cd^^Yb`b`cc``c\accccZT`YTbYb`Y\VZYBBa\Y
+SEQ: GCCGAGTAGCGTTCNTGGNTACCTTCCGATCCGCGGCCCGCCCCCTGTCT
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: AANAANANCTNCNNANCGNCGGTTTCGTNANNANNGGTTCGCANCGNNNC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2
+---

diff --git a/bp_test/test/test_order_pairs b/bp_test/test/test_order_pairs
new file mode 100755 (executable)
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_order_pairs
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean