From 40a9c05afcf4ec3136df7f0f629cca7287cf0d6a Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 17 Jan 2011 16:02:32 +0000
Subject: [PATCH 1/1] added tests for find_gaps

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1208 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/find_gaps            |   4 +--
 bp_test/in/find_gaps.in     |  39 ++++++++++++++++++++
 bp_test/out/find_gaps.out.1 |  54 ++++++++++++++++++++++++++++
 bp_test/out/find_gaps.out.2 |  69 ++++++++++++++++++++++++++++++++++++
 bp_test/test/test_find_gaps |  11 ++++++
 code_python/Cjung/Args.pyc  | Bin 5364 -> 5375 bytes
 6 files changed, 175 insertions(+), 2 deletions(-)
 create mode 100644 bp_test/in/find_gaps.in
 create mode 100644 bp_test/out/find_gaps.out.1
 create mode 100644 bp_test/out/find_gaps.out.2
 create mode 100755 bp_test/test/test_find_gaps

diff --git a/bp_bin/find_gaps b/bp_bin/find_gaps
index f885f82..300ae09 100755
--- a/bp_bin/find_gaps
+++ b/bp_bin/find_gaps
@@ -47,6 +47,8 @@ $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
+    Maasha::Biopieces::put_record( $record, $out );
+
     if ( exists $record->{ 'SEQ' } )
     {
         $gaps = find_gaps( $record->{ 'SEQ' }, $options->{ 'min_len' } );
@@ -58,8 +60,6 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
             Maasha::Biopieces::put_record( $gap, $out ); 
         }
     }
-
-    Maasha::Biopieces::put_record( $record, $out );
 }
 
 Maasha::Biopieces::close_stream( $in );
diff --git a/bp_test/in/find_gaps.in b/bp_test/in/find_gaps.in
new file mode 100644
index 0000000..da54d8d
--- /dev/null
+++ b/bp_test/in/find_gaps.in
@@ -0,0 +1,39 @@
+SEQ: NNNNNNNNNNtatcgatcgatcgaacgt
+SEQ_LEN: 28
+SEQ_NAME: test1
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+SEQ: tatcgatcgatcgaacgtnnnnnnnnnn
+SEQ_LEN: 28
+SEQ_NAME: test2
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+SEQ: tatcgatcNNNNNNNNNNgatcgaacgt
+SEQ_LEN: 28
+SEQ_NAME: test3
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+SEQ: NNNNtatcgatcgatcgaacgt
+SEQ_LEN: 22
+SEQ_NAME: test4
+---
+SEQ: tatcgatcgatcgaacgtnnnn
+SEQ_LEN: 22
+SEQ_NAME: test5
+---
+SEQ: tatcgatcNNNNgatcgaacgt
+SEQ_LEN: 22
+SEQ_NAME: test6
+---
diff --git a/bp_test/out/find_gaps.out.1 b/bp_test/out/find_gaps.out.1
new file mode 100644
index 0000000..143b6d0
--- /dev/null
+++ b/bp_test/out/find_gaps.out.1
@@ -0,0 +1,54 @@
+SEQ: NNNNNNNNNNtatcgatcgatcgaacgt
+SEQ_NAME: test1
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+SEQ: tatcgatcgatcgaacgtnnnnnnnnnn
+SEQ_NAME: test2
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+SEQ: tatcgatcNNNNNNNNNNgatcgaacgt
+SEQ_NAME: test3
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+SEQ: NNNNtatcgatcgatcgaacgt
+SEQ_NAME: test4
+SEQ_LEN: 22
+---
+SEQ: tatcgatcgatcgaacgtnnnn
+SEQ_NAME: test5
+SEQ_LEN: 22
+---
+SEQ: tatcgatcNNNNgatcgaacgt
+SEQ_NAME: test6
+SEQ_LEN: 22
+---
diff --git a/bp_test/out/find_gaps.out.2 b/bp_test/out/find_gaps.out.2
new file mode 100644
index 0000000..7f8abf9
--- /dev/null
+++ b/bp_test/out/find_gaps.out.2
@@ -0,0 +1,69 @@
+SEQ: NNNNNNNNNNtatcgatcgatcgaacgt
+SEQ_NAME: test1
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+S_LEN: 10
+S_ID: test1
+S_BEG: 0
+S_END: 9
+---
+SEQ: tatcgatcgatcgaacgtnnnnnnnnnn
+SEQ_NAME: test2
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+S_LEN: 10
+S_ID: test2
+S_BEG: 18
+S_END: 27
+---
+SEQ: tatcgatcNNNNNNNNNNgatcgaacgt
+SEQ_NAME: test3
+SEQ_LEN: 28
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+S_LEN: 10
+S_ID: test3
+S_BEG: 8
+S_END: 17
+---
+SEQ: NNNNtatcgatcgatcgaacgt
+SEQ_NAME: test4
+SEQ_LEN: 22
+---
+S_LEN: 4
+S_ID: test4
+S_BEG: 0
+S_END: 3
+---
+SEQ: tatcgatcgatcgaacgtnnnn
+SEQ_NAME: test5
+SEQ_LEN: 22
+---
+S_LEN: 4
+S_ID: test5
+S_BEG: 18
+S_END: 21
+---
+SEQ: tatcgatcNNNNgatcgaacgt
+SEQ_NAME: test6
+SEQ_LEN: 22
+---
+S_LEN: 4
+S_ID: test6
+S_BEG: 8
+S_END: 11
+---
diff --git a/bp_test/test/test_find_gaps b/bp_test/test/test_find_gaps
new file mode 100755
index 0000000..939c6f4
--- /dev/null
+++ b/bp_test/test/test_find_gaps
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in -m 3 -O $tmp"
+assert_no_diff $tmp $out.2
+clean
diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index ddc36fc600f13f1a86a119e0c8fadcd00d0064e1..4c39c4a68733e7fdac49e939fe26d08e98449439 100644
GIT binary patch
delta 224
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z*hlUUXxb)=@t#8#`pB)bS(48lS=Z)7ehk|t3kmK<(>9q&s1{9V^A@2K$R>f@K6#^v
FGXQ#$LC^pI

delta 217
zcmeyb`9+iC;wN6NjZrS%8#yxAI1LyW81yspb5kcz5HZ-iimieXO(=%rIjWG(=1Q(2
zR3Yuj3Oq+q^yy5N<~@fZqP<y;&jD4N&gLon0cb*#r381Q>YL0ZREH|Ed9Tn(RBibH
D%c4DY

-- 
2.39.2