From cb41f472b532613a00a69d2cb03afc88d4f4811d Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 23 Sep 2013 11:48:35 +0000
Subject: [PATCH] created find_orphans Biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2205 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/find_orphans            | 81 ++++++++++++++++++++++++++++++++++
 bp_test/in/find_orphans.in.1   | 55 +++++++++++++++++++++++
 bp_test/in/find_orphans.in.2   | 10 +++++
 bp_test/out/find_orphans.out.1 | 66 +++++++++++++++++++++++++++
 bp_test/out/find_orphans.out.2 | 12 +++++
 bp_test/test/test_find_orphans | 11 +++++
 6 files changed, 235 insertions(+)
 create mode 100755 bp_bin/find_orphans
 create mode 100644 bp_test/in/find_orphans.in.1
 create mode 100644 bp_test/in/find_orphans.in.2
 create mode 100644 bp_test/out/find_orphans.out.1
 create mode 100644 bp_test/out/find_orphans.out.2
 create mode 100755 bp_test/test/test_find_orphans

diff --git a/bp_bin/find_orphans b/bp_bin/find_orphans
new file mode 100755
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__
diff --git a/bp_test/in/find_orphans.in.1 b/bp_test/in/find_orphans.in.1
new file mode 100644
index 0000000..26199b7
--- /dev/null
+++ b/bp_test/in/find_orphans.in.1
@@ -0,0 +1,55 @@
+SCORES: 5<9=<@@@@@@@CC#######6666C>ECD
+SEQ: GCAGCAGCTCCAGANNNNNNNCGTTGATCA
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:16206:1411 2:N:0:1
+SEQ_LEN: 30
+---
+SCORES: ??????@@DDDDBDDDGFGGGFHIIHFHHE
+SEQ: ACAGCCGCACCATGTAGTTCCAGCCGGCCA
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:15796:1414 1:N:0:1
+SEQ_LEN: 30
+---
+SCORES: 5<=====@@@@@5<@CE#######666CEC
+SEQ: ATGCGATCAAGGTCCAGNNNNNNNCGCCGG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:15796:1414 2:N:0:1
+SEQ_LEN: 30
+---
+SCORES: ?????@=@B<@DD7?@C5CCCFFFECCAF;
+SEQ: GATGCGGCGTTCGCACGCAGTGCCGAATTG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:17415:1426 1:N:0:1
+SEQ_LEN: 30
+---
+SCORES: ?????BB9<B<?BBB???FFFFFHHHHHFH
+SEQ: GGTAACAAGTACCTCTCCAAGATGTACAAC
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:14110:1429 1:N:0:1
+SEQ_LEN: 30
+---
+SCORES: 5<===>>A@@@@@+<>CEEACE.CCEEEBF
+SEQ: ATCTTTGACGCGGCTAAACAGATATTCAGC
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:14110:1429 2:N:0:1
+SEQ_LEN: 30
+---
+SCORES: 5<???BBDBBBBBDDCAFFFFFH?EF>>C@
+SEQ: TCTCATCGGAAACGGTGAAGTCACACCTGG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:16811:1432 2:N:0:1
+SEQ_LEN: 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: 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
+---
diff --git a/bp_test/in/find_orphans.in.2 b/bp_test/in/find_orphans.in.2
new file mode 100644
index 0000000..265e2d0
--- /dev/null
+++ b/bp_test/in/find_orphans.in.2
@@ -0,0 +1,10 @@
+SCORES: 5<===>>A@@@@@+<>CEEACE.CCEEEBF
+SEQ: ATCTTTGACGCGGCTAAACAGATATTCAGC
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:14110:1429 2:N:0:1
+SEQ_LEN: 30
+---
+SCORES: 5<???BBDBBBBBDDCAFFFFFH?EF>>C@
+SEQ: TCTCATCGGAAACGGTGAAGTCACACCTGG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:16811:1432 2:N:0:1
+SEQ_LEN: 30
+---
diff --git a/bp_test/out/find_orphans.out.1 b/bp_test/out/find_orphans.out.1
new file mode 100644
index 0000000..bb5e493
--- /dev/null
+++ b/bp_test/out/find_orphans.out.1
@@ -0,0 +1,66 @@
+SCORES: 5<9=<@@@@@@@CC#######6666C>ECD
+SEQ: GCAGCAGCTCCAGANNNNNNNCGTTGATCA
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:16206:1411 2:N:0:1
+SEQ_LEN: 30
+TYPE: orphan
+---
+SCORES: ??????@@DDDDBDDDGFGGGFHIIHFHHE
+SEQ: ACAGCCGCACCATGTAGTTCCAGCCGGCCA
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:15796:1414 1:N:0:1
+SEQ_LEN: 30
+TYPE: paired
+---
+SCORES: 5<=====@@@@@5<@CE#######666CEC
+SEQ: ATGCGATCAAGGTCCAGNNNNNNNCGCCGG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:15796:1414 2:N:0:1
+SEQ_LEN: 30
+TYPE: paired
+---
+SCORES: ?????@=@B<@DD7?@C5CCCFFFECCAF;
+SEQ: GATGCGGCGTTCGCACGCAGTGCCGAATTG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:17415:1426 1:N:0:1
+SEQ_LEN: 30
+TYPE: orphan
+---
+SCORES: ?????BB9<B<?BBB???FFFFFHHHHHFH
+SEQ: GGTAACAAGTACCTCTCCAAGATGTACAAC
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:14110:1429 1:N:0:1
+SEQ_LEN: 30
+TYPE: paired
+---
+SCORES: 5<===>>A@@@@@+<>CEEACE.CCEEEBF
+SEQ: ATCTTTGACGCGGCTAAACAGATATTCAGC
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:14110:1429 2:N:0:1
+SEQ_LEN: 30
+TYPE: paired
+---
+SCORES: 5<???BBDBBBBBDDCAFFFFFH?EF>>C@
+SEQ: TCTCATCGGAAACGGTGAAGTCACACCTGG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:16811:1432 2:N:0:1
+SEQ_LEN: 30
+TYPE: orphan
+---
+SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB
+SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1
+TYPE: orphan
+---
+SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB
+SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1
+TYPE: paired
+---
+SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2
+TYPE: paired
+---
+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
+TYPE: orphan
+---
diff --git a/bp_test/out/find_orphans.out.2 b/bp_test/out/find_orphans.out.2
new file mode 100644
index 0000000..a537b17
--- /dev/null
+++ b/bp_test/out/find_orphans.out.2
@@ -0,0 +1,12 @@
+SCORES: 5<===>>A@@@@@+<>CEEACE.CCEEEBF
+SEQ: ATCTTTGACGCGGCTAAACAGATATTCAGC
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:14110:1429 2:N:0:1
+SEQ_LEN: 30
+TYPE: orphan
+---
+SCORES: 5<???BBDBBBBBDDCAFFFFFH?EF>>C@
+SEQ: TCTCATCGGAAACGGTGAAGTCACACCTGG
+SEQ_NAME: M01168:19:000000000-A2YGD:1:1101:16811:1432 2:N:0:1
+SEQ_LEN: 30
+TYPE: orphan
+---
diff --git a/bp_test/test/test_find_orphans b/bp_test/test/test_find_orphans
new file mode 100755
index 0000000..b0304c9
--- /dev/null
+++ b/bp_test/test/test_find_orphans
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in.1 -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in.2 -O $tmp"
+assert_no_diff $tmp $out.2
+clean
-- 
2.39.2