From: martinahansen Date: Mon, 23 May 2011 19:49:44 +0000 (+0000) Subject: fixed find_adaptor tests X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=b9838651d610686803c9c32a35b00d11fd560649;p=biopieces.git 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 960ea22..8bf5394 100644 --- 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 a177def..f59114e 100644 --- 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 caa02d4..c5eb741 100644 --- 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 6592f45..029538b 100644 --- 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 cdfc701..8da18a4 100644 --- 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 292aebf..a337be4 100644 --- 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 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 a769cfd..cbbe4a7 100755 --- 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