From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 8 Mar 2013 14:39:37 +0000 (+0000)
Subject: added new Biopiece merge_pair_seq
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=128ec42589b930642cf8863baa8a844dc5fd2c3f

added new Biopiece merge_pair_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2120 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_test/in/merge_pair_seq.in b/bp_test/in/merge_pair_seq.in
new file mode 100644
index 0000000..9129ea8
--- /dev/null
+++ b/bp_test/in/merge_pair_seq.in
@@ -0,0 +1,50 @@
+SCORES: <??????BDDDDDDDDGGGG
+SEQ: TGGGGAATATTGGACAATGG
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14
+---
+SCORES: ?????BB<-<BDDDDDFEEF
+SEQ: CCTGTTTGCTACCCACGCTT
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14
+---
+SCORES: <???9?BBBDBDDBDDFFFF
+SEQ: TAGGGAATCTTGCACAATGG
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14
+---
+SCORES: ,5<??BB?DDABDBDDFFFF
+SEQ: ACTCTTCGCTACCCATGCTT
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14
+---
+SCORES: ?????BBBBBDDBDDBFFFF
+SEQ: TAGGGAATCTTGCACAATGG
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14
+---
+SCORES: ??,<??B?BB?BBBBBFF?F
+SEQ: CCTCTTCGCTACCCATGCTT
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 2:N:0:14
+---
+SCORES: 5<???B-<-?<BBBBBFFF;
+SEQ: TAGGGAATCTTGCACAATGG
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:17246:2253 1:N:0:14
+---
+SCORES: ?????BB??BBDBBBBBFFF
+SEQ: CCTCTTCGCTACCCATGCTT
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:17246:2253 2:N:0:14
+---
+SCORES: 55?????B?BB<-5@BC9CF
+SEQ: TGGGGAATTTTGCGCAATGG
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13072:2276 1:N:0:14
+---
+SCORES: ,<5<<<>>-5-@@@@@CEEE
+SEQ: CCTGTTTGCTCCCCACGCTT
+SEQ_LEN: 20
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13072:2276 2:N:0:14
+---
diff --git a/bp_test/out/merge_pair_seq.out.1 b/bp_test/out/merge_pair_seq.out.1
new file mode 100644
index 0000000..14ba679
--- /dev/null
+++ b/bp_test/out/merge_pair_seq.out.1
@@ -0,0 +1,35 @@
+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
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:17246:2253 1:N:0:14
+SEQ: TAGGGAATCTTGCACAATGGCCTCTTCGCTACCCATGCTT
+SEQ_LEN: 40
+SCORES: 5<???B-<-?<BBBBBFFF;?????BB??BBDBBBBBFFF
+SEQ_LEN_LEFT: 20
+SEQ_LEN_RIGHT: 20
+---
+SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13072:2276 1:N:0:14
+SEQ: TGGGGAATTTTGCGCAATGGCCTGTTTGCTCCCCACGCTT
+SEQ_LEN: 40
+SCORES: 55?????B?BB<-5@BC9CF,<5<<<>>-5-@@@@@CEEE
+SEQ_LEN_LEFT: 20
+SEQ_LEN_RIGHT: 20
+---
diff --git a/bp_test/test/test_merge_pair_seq b/bp_test/test/test_merge_pair_seq
new file mode 100755
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_merge_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/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index eab90cb..b3bdd79 100755
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -373,6 +373,18 @@ class TestSeq < Test::Unit::TestCase
     assert_equal("HHHHIIII", @entry.qual)
   end
 
+  test "#[] returns correctly" do
+    @entry.seq  = "atcg"
+    @entry.type = :dna
+    @entry.qual = "FGHI"
+
+    fail
+  end
+
+  test "[]= returns correctly" do
+    fail
+  end
+
   test "#subseq with start < 0 raises" do
     @entry.seq = "ATCG"
     assert_raise(SeqError) { @entry.subseq(-1, 1) }