From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 8 Mar 2013 18:42:08 +0000 (+0000)
Subject: added split_pair_seq biopiece
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=4148425e5c7f540c34a2be6cfe19bb89d16a54cb

added split_pair_seq biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2122 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/merge_pair_seq b/bp_bin/merge_pair_seq
index 56c296e..1bd0214 100755
--- a/bp_bin/merge_pair_seq
+++ b/bp_bin/merge_pair_seq
@@ -24,7 +24,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Join sequences in the stream.
+# Merge pair-end sequences in the stream.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -78,7 +78,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
           new_record[:SEQ_LEN_RIGHT] = seq_len_right
           output.puts new_record
         else
-          raise "names mismatch: #{entry1.seq_name} != #{entry2.seq_name}"
+          raise "name mismatch: #{entry1.seq_name} != #{entry2.seq_name}"
         end
 
         entry1 = nil
diff --git a/bp_bin/split_pair_seq b/bp_bin/split_pair_seq
new file mode 100755
index 0000000..b0425ac
--- /dev/null
+++ b/bp_bin/split_pair_seq
@@ -0,0 +1,72 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Split joined pair-end sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/seq'
+require 'pp'
+
+options = Biopieces.options_parse(ARGV)
+
+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[:SEQ_LEN_LEFT] and record[:SEQ_LEN_RIGHT]
+      entry = Seq.new_bp(record)
+
+      len_left  = record[:SEQ_LEN_LEFT].to_i
+      len_right = record[:SEQ_LEN_RIGHT].to_i
+
+      unless len_left + len_right == entry.length
+        raise "SEQ_LEN_LEFT + SEQ_LEN_RIGHT != SEQ_LEN #{len_left} + #{len_right} != #{entry.length}"
+      end
+
+      entry1 = entry.subseq(0, len_left)
+      entry2 = entry.subseq(len_left)
+
+      if entry.seq_name =~ /^[^ ]+ \d:/
+        entry2.seq_name.sub!(/ \d:/, " 2:")
+      elsif entry.seq_name =~ /^.+\/\d$/
+        entry2.seq_name[-1] = "2"
+      else
+        raise "Could not match sequence name: #{entry.seq_name}"
+      end
+
+      output.puts entry1.to_bp
+      output.puts entry2.to_bp
+    else
+      output.puts record
+    end
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
diff --git a/bp_test/in/split_pair_seq.in b/bp_test/in/split_pair_seq.in
new file mode 100644
index 0000000..2370d3b
--- /dev/null
+++ b/bp_test/in/split_pair_seq.in
@@ -0,0 +1,21 @@
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14
+SEQ: TGGGGAATATTGGACAATGGCCTGTTTGCTACCCACGCTT
+SEQ_LEN: 40
+SCORES: <??????BDDDDDDDDGGGG?????BB<-<BDDDDDFEEF
+SEQ_LEN_LEFT: 20
+SEQ_LEN_RIGHT: 20
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGGACTCTTCGCTACCCATGCTT
+SEQ_LEN: 40
+SCORES: <???9?BBBDBDDBDDFFFF,5<??BB?DDABDBDDFFFF
+SEQ_LEN_LEFT: 20
+SEQ_LEN_RIGHT: 20
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGGCCTCTTCGCTACCCATGCTT
+SEQ_LEN: 40
+SCORES: ?????BBBBBDDBDDBFFFF??,<??B?BB?BBBBBFF?F
+SEQ_LEN_LEFT: 20
+SEQ_LEN_RIGHT: 20
+---
diff --git a/bp_test/out/split_pair_seq.out.1 b/bp_test/out/split_pair_seq.out.1
new file mode 100644
index 0000000..abccad6
--- /dev/null
+++ b/bp_test/out/split_pair_seq.out.1
@@ -0,0 +1,30 @@
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14
+SEQ: TGGGGAATATTGGACAATGG
+SEQ_LEN: 20
+SCORES: <??????BDDDDDDDDGGGG
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14
+SEQ: CCTGTTTGCTACCCACGCTT
+SEQ_LEN: 20
+SCORES: ?????BB<-<BDDDDDFEEF
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGG
+SEQ_LEN: 20
+SCORES: <???9?BBBDBDDBDDFFFF
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14
+SEQ: ACTCTTCGCTACCCATGCTT
+SEQ_LEN: 20
+SCORES: ,5<??BB?DDABDBDDFFFF
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGG
+SEQ_LEN: 20
+SCORES: ?????BBBBBDDBDDBFFFF
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 2:N:0:14
+SEQ: CCTCTTCGCTACCCATGCTT
+SEQ_LEN: 20
+SCORES: ??,<??B?BB?BBBBBFF?F
+---
diff --git a/bp_test/test/test_split_pair_seq b/bp_test/test/test_split_pair_seq
new file mode 100755
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_split_pair_seq
@@ -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
diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 92ce19e..f76466f 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -444,7 +444,9 @@ class Seq
       qual = self.qual[start .. stop] unless self.qual.nil?
     end
 
-    Seq.new(self.seq_name, seq, self.type, qual)    # TODO changed self.seq_name.dup to self.seq_name -> consequence?
+    seq_name = self.seq_name.nil? ? nil : self.seq_name.dup
+
+    Seq.new(seq_name, seq, self.type, qual)
   end
 
   # Method that replaces a sequence with a subsequence from a given start position