From: martinahansen Date: Mon, 18 Apr 2011 12:32:34 +0000 (+0000) Subject: added tests for find_adaptor X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=49b720a89d785d285bf0ac5f9260c31f5b612ee3;p=biopieces.git added tests for find_adaptor git-svn-id: http://biopieces.googlecode.com/svn/trunk@1336 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_test/in/find_adaptor.in b/bp_test/in/find_adaptor.in new file mode 100644 index 0000000..960ea22 --- /dev/null +++ b/bp_test/in/find_adaptor.in @@ -0,0 +1,32 @@ +SEQ_NAME: test_full_length_adaptor +SEQ: TCGTATGCCGTCTTCTGCTTG +SEQ_LEN: 21 +--- +SEQ_NAME: test_begin_match +SEQ: TCGTATGCCGTCTTCTGCTTGactacgt +SEQ_LEN: 28 +--- +SEQ_NAME: test_middle_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt +SEQ_LEN: 37 +--- +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 +--- diff --git a/bp_test/out/find_adaptor.out.1 b/bp_test/out/find_adaptor.out.1 new file mode 100644 index 0000000..a177def --- /dev/null +++ b/bp_test/out/find_adaptor.out.1 @@ -0,0 +1,56 @@ +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 +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 +--- diff --git a/bp_test/out/find_adaptor.out.2 b/bp_test/out/find_adaptor.out.2 new file mode 100644 index 0000000..caa02d4 --- /dev/null +++ b/bp_test/out/find_adaptor.out.2 @@ -0,0 +1,53 @@ +SEQ_NAME: test_full_length_adaptor +SEQ: TCGTATGCCGTCTTCTGCTTG +SEQ_LEN: 21 +--- +SEQ_NAME: test_begin_match +SEQ: TCGTATGCCGTCTTCTGCTTGactacgt +SEQ_LEN: 28 +ADAPTOR_POS: 24 +ADAPTOR_LEN: 4 +ADAPTOR_MATCH: acgt +--- +SEQ_NAME: test_middle_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt +SEQ_LEN: 37 +ADAPTOR_POS: 33 +ADAPTOR_LEN: 4 +ADAPTOR_MATCH: acgt +--- +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_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 +--- diff --git a/bp_test/out/find_adaptor.out.3 b/bp_test/out/find_adaptor.out.3 new file mode 100644 index 0000000..6592f45 --- /dev/null +++ b/bp_test/out/find_adaptor.out.3 @@ -0,0 +1,56 @@ +SEQ_NAME: test_full_length_adaptor +SEQ: TCGTATGCCGTCTTCTGCTTG +SEQ_LEN: 21 +ADAPTOR_POS: 0 +ADAPTOR_LEN: 17 +ADAPTOR_MATCH: TCGTATGCCGTCTTCTG +--- +SEQ_NAME: test_begin_match +SEQ: TCGTATGCCGTCTTCTGCTTGactacgt +SEQ_LEN: 28 +ADAPTOR_POS: 0 +ADAPTOR_LEN: 17 +ADAPTOR_MATCH: TCGTATGCCGTCTTCTG +--- +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 +--- diff --git a/bp_test/out/find_adaptor.out.4 b/bp_test/out/find_adaptor.out.4 new file mode 100644 index 0000000..cdfc701 --- /dev/null +++ b/bp_test/out/find_adaptor.out.4 @@ -0,0 +1,53 @@ +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 +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 +--- diff --git a/bp_test/out/find_adaptor.out.5 b/bp_test/out/find_adaptor.out.5 new file mode 100644 index 0000000..292aebf --- /dev/null +++ b/bp_test/out/find_adaptor.out.5 @@ -0,0 +1,56 @@ +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 +ADAPTOR_POS: 9 +ADAPTOR_LEN: 19 +ADAPTOR_MATCH: TCGGATGCGGTCTCATGTT +--- +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 +--- diff --git a/bp_test/test/test_find_adaptor b/bp_test/test/test_find_adaptor new file mode 100755 index 0000000..8308f65 --- /dev/null +++ b/bp_test/test/test_find_adaptor @@ -0,0 +1,23 @@ +#!/bin/bash + +source "$BP_DIR/bp_test/lib/test.sh" + +run "$bp -a TCGTATGCCGTCTTCTGCTTG -I $in -O $tmp" +assert_no_diff $tmp $out.1 +clean + +run "$bp -a TCGTATGCCGTCTTCTGCTTG -p 25 -I $in -O $tmp" +assert_no_diff $tmp $out.2 +clean + +run "$bp -a TCGTATGCCGTCTTCTGCTTG -p -35 -I $in -O $tmp" +assert_no_diff $tmp $out.3 +clean + +run "$bp -a TCGTATGCCGTCTTCTGCTTG -e 5 -I $in -O $tmp" +assert_no_diff $tmp $out.4 +clean + +run "$bp -a TCGTATGCCGTCTTCTGCTTG -e 30 -I $in -O $tmp" +assert_no_diff $tmp $out.5 +clean