From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 17 Jan 2011 16:02:32 +0000 (+0000)
Subject: added tests for find_gaps
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=40a9c05afcf4ec3136df7f0f629cca7287cf0d6a;p=biopieces.git

added tests for find_gaps

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1208 74ccb610-7750-0410-82ae-013aeee3265d
---

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 ddc36fc..4c39c4a 100644
Binary files a/code_python/Cjung/Args.pyc and b/code_python/Cjung/Args.pyc differ