fixed find_adaptor tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1419 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/find_adaptor.in b/bp_test/in/find_adaptor.in
index 960ea228ef4281b270d055bb0b9b674eeb4df40b..8bf5394295ae9414833824c8e45ea1c60c5c21f2 100644 (file)
--- a/bp_test/in/find_adaptor.in
+++ b/bp_test/in/find_adaptor.in
@@ -14,19 +14,19 @@ SEQ_NAME: test_end_match
 SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 27
 ---
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
-SEQ_LEN: 36
----
 SEQ_NAME: test_end_trim
 SEQ: gtgacactatcgatacgatcgacactgaTCGTA
 SEQ_LEN: 33
 ---
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
+SEQ_NAME: test_mismatches
+SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_insertions
+SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_deletions
+SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
+SEQ_LEN: 37
 ---

diff --git a/bp_test/out/find_adaptor.out.1 b/bp_test/out/find_adaptor.out.1
index a177def7c1a1038e3c346dff8faab999cb8ddaf6..f59114ee0809f628ffb48a6a12e615d92af46af4 100644 (file)
--- a/bp_test/out/find_adaptor.out.1
+++ b/bp_test/out/find_adaptor.out.1
@@ -3,54 +3,38 @@ SEQ: TCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 21
 ADAPTOR_POS: 0
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_begin_match
 SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 28
 ADAPTOR_POS: 0
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_middle_match
 SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 37
 ADAPTOR_POS: 9
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_end_match
 SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 27
 ADAPTOR_POS: 6
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
-SEQ_LEN: 36
-ADAPTOR_POS: 32
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: acgt
 ---
 SEQ_NAME: test_end_trim
 SEQ: gtgacactatcgatacgatcgacactgaTCGTA
 SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTA
 ---
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: TCGT
+SEQ_NAME: test_mismatches
+SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_insertions
+SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_deletions
+SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
+SEQ_LEN: 37
 ---

diff --git a/bp_test/out/find_adaptor.out.2 b/bp_test/out/find_adaptor.out.2
index caa02d4769356dedb42587f0ff414078268b723a..c5eb741e9b12a519f156c15e282c916293775ab8 100644 (file)
--- a/bp_test/out/find_adaptor.out.2
+++ b/bp_test/out/find_adaptor.out.2
@@ -1,53 +1,42 @@
 SEQ_NAME: test_full_length_adaptor
 SEQ: TCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 21
+ADAPTOR_POS: 0
+ADAPTOR_LEN: 21
 ---
 SEQ_NAME: test_begin_match
 SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 28
-ADAPTOR_POS: 24
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: acgt
+ADAPTOR_POS: 0
+ADAPTOR_LEN: 21
 ---
 SEQ_NAME: test_middle_match
 SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 37
-ADAPTOR_POS: 33
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: acgt
+ADAPTOR_POS: 9
+ADAPTOR_LEN: 21
 ---
 SEQ_NAME: test_end_match
 SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 27
-ADAPTOR_POS: 24
-ADAPTOR_LEN: 3
-ADAPTOR_MATCH: TTG
----
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
-ADAPTOR_POS: 33
+ADAPTOR_POS: 6
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
-SEQ_LEN: 36
-ADAPTOR_POS: 32
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: acgt
 ---
 SEQ_NAME: test_end_trim
 SEQ: gtgacactatcgatacgatcgacactgaTCGTA
 SEQ_LEN: 33
 ADAPTOR_POS: 28
 ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTA
 ---
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: TCGT
+SEQ_NAME: test_mismatches
+SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_insertions
+SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_deletions
+SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
+SEQ_LEN: 37
 ---

diff --git a/bp_test/out/find_adaptor.out.3 b/bp_test/out/find_adaptor.out.3
index 6592f457fc00886e4bdbc1e94ad526b627ac8cd9..029538b5d743a8372699f7d2eb16dd8dc15ff332 100644 (file)
--- a/bp_test/out/find_adaptor.out.3
+++ b/bp_test/out/find_adaptor.out.3
@@ -2,55 +2,41 @@ SEQ_NAME: test_full_length_adaptor
 SEQ: TCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 21
 ADAPTOR_POS: 0
-ADAPTOR_LEN: 17
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTG
+ADAPTOR_LEN: 21
 ---
 SEQ_NAME: test_begin_match
 SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 28
 ADAPTOR_POS: 0
-ADAPTOR_LEN: 17
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTG
+ADAPTOR_LEN: 21
 ---
 SEQ_NAME: test_middle_match
 SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 37
 ADAPTOR_POS: 9
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_end_match
 SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 27
 ADAPTOR_POS: 6
-ADAPTOR_LEN: 17
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTG
----
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
-ADAPTOR_POS: 33
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
-SEQ_LEN: 36
-ADAPTOR_POS: 32
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: acgt
 ---
 SEQ_NAME: test_end_trim
 SEQ: gtgacactatcgatacgatcgacactgaTCGTA
 SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTA
 ---
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: TCGT
+SEQ_NAME: test_mismatches
+SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
+SEQ_LEN: 37
+ADAPTOR_POS: 9
+ADAPTOR_LEN: 21
+---
+SEQ_NAME: test_insertions
+SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_deletions
+SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
+SEQ_LEN: 37
 ---

diff --git a/bp_test/out/find_adaptor.out.4 b/bp_test/out/find_adaptor.out.4
index cdfc701c08745da3a5918e1010b43ed6c17ec505..8da18a48462dcff23bed8c0a8b70d83197952d44 100644 (file)
--- a/bp_test/out/find_adaptor.out.4
+++ b/bp_test/out/find_adaptor.out.4
@@ -3,51 +3,40 @@ SEQ: TCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 21
 ADAPTOR_POS: 0
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_begin_match
 SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 28
 ADAPTOR_POS: 0
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_middle_match
 SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 37
 ADAPTOR_POS: 9
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_end_match
 SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 27
 ADAPTOR_POS: 6
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
-SEQ_LEN: 36
-ADAPTOR_POS: 35
-ADAPTOR_LEN: 1
-ADAPTOR_MATCH: T
 ---
 SEQ_NAME: test_end_trim
 SEQ: gtgacactatcgatacgatcgacactgaTCGTA
 SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTA
 ---
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
+SEQ_NAME: test_mismatches
+SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_insertions
+SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
+SEQ_LEN: 37
+ADAPTOR_POS: 9
+ADAPTOR_LEN: 19
+---
+SEQ_NAME: test_deletions
+SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
+SEQ_LEN: 37
 ---

diff --git a/bp_test/out/find_adaptor.out.5 b/bp_test/out/find_adaptor.out.5
index 292aebf786fb8410583615a4667a09429ad62578..a337be4b10d91a831eebe31ca423e0aef093d773 100644 (file)
--- a/bp_test/out/find_adaptor.out.5
+++ b/bp_test/out/find_adaptor.out.5
@@ -3,54 +3,40 @@ SEQ: TCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 21
 ADAPTOR_POS: 0
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_begin_match
 SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 28
 ADAPTOR_POS: 0
 ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
 ---
 SEQ_NAME: test_middle_match
 SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
 SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
+ADAPTOR_POS: 7
+ADAPTOR_LEN: 23
 ---
 SEQ_NAME: test_end_match
 SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
 SEQ_LEN: 27
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
-SEQ_LEN: 36
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 19
-ADAPTOR_MATCH: TCGGATGCGGTCTCATGTT
+ADAPTOR_POS: 4
+ADAPTOR_LEN: 23
 ---
 SEQ_NAME: test_end_trim
 SEQ: gtgacactatcgatacgatcgacactgaTCGTA
 SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTA
 ---
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTG
+SEQ_NAME: test_mismatches
+SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_insertions
+SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
+SEQ_LEN: 37
+---
+SEQ_NAME: test_deletions
+SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
+SEQ_LEN: 37
+ADAPTOR_POS: 9
+ADAPTOR_LEN: 23
 ---

diff --git a/bp_test/out/find_adaptor.out.6 b/bp_test/out/find_adaptor.out.6
deleted file mode 100644 (file)
index 45197a2..0000000
--- a/bp_test/out/find_adaptor.out.6
+++ /dev/null
@@ -1,50 +0,0 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_end_match
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 27
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
-SEQ_LEN: 36
----
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTA
----
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
----

diff --git a/bp_test/test/test_find_adaptor b/bp_test/test/test_find_adaptor
index a769cfd0c4329839c044b45fa100e51e691ea5e6..cbbe4a79a2d08744b9dccc51e8d6d65af68cea7f 100755 (executable)
--- a/bp_test/test/test_find_adaptor
+++ b/bp_test/test/test_find_adaptor
@@ -2,26 +2,22 @@
 
 source "$BP_DIR/bp_test/lib/test.sh"
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -I $in -O $tmp"
+run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 0 -I $in -O $tmp"
 assert_no_diff $tmp $out.1
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -p 25 -I $in -O $tmp"
+run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 0 -p -l 5 -I $in -O $tmp"
 assert_no_diff $tmp $out.2
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -p -35 -I $in -O $tmp"
+run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 10 -i 0 -d 0 -I $in -O $tmp"
 assert_no_diff $tmp $out.3
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -e 5 -I $in -O $tmp"
+run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 10 -d 0 -I $in -O $tmp"
 assert_no_diff $tmp $out.4
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -e 30 -I $in -O $tmp"
+run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 10 -I $in -O $tmp"
 assert_no_diff $tmp $out.5
 clean
-
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -e 0 -d 5 -I $in -O $tmp"
-assert_no_diff $tmp $out.6
-clean