From 179c4cb32087fcdda2dffe5826fadbfd9e112c88 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 3 Sep 2012 11:29:11 +0000 Subject: [PATCH] updated testing files for find_adaptor and clip_adaptor git-svn-id: http://biopieces.googlecode.com/svn/trunk@1907 74ccb610-7750-0410-82ae-013aeee3265d --- bp_test/in/clip_adaptor.in | 33 +++++-- bp_test/in/find_adaptor.in | 102 ++++++++++++++----- bp_test/out/clip_adaptor.out.1 | 33 +++++-- bp_test/out/find_adaptor.out.1 | 134 ++++++++++++++++++------- bp_test/out/find_adaptor.out.10 | 130 ++++++++++++++++++++++++ bp_test/out/find_adaptor.out.2 | 138 ++++++++++++++++++-------- bp_test/out/find_adaptor.out.3 | 144 +++++++++++++++++++-------- bp_test/out/find_adaptor.out.4 | 138 ++++++++++++++++++-------- bp_test/out/find_adaptor.out.5 | 162 ++++++++++++++++++++++-------- bp_test/out/find_adaptor.out.6 | 133 +++++++++++++++++++++++++ bp_test/out/find_adaptor.out.7 | 169 ++++++++++++++++++++++++++++++++ bp_test/out/find_adaptor.out.8 | 130 ++++++++++++++++++++++++ bp_test/out/find_adaptor.out.9 | 130 ++++++++++++++++++++++++ bp_test/test/test_find_adaptor | 30 +++++- 14 files changed, 1370 insertions(+), 236 deletions(-) create mode 100644 bp_test/out/find_adaptor.out.10 create mode 100644 bp_test/out/find_adaptor.out.6 create mode 100644 bp_test/out/find_adaptor.out.7 create mode 100644 bp_test/out/find_adaptor.out.8 create mode 100644 bp_test/out/find_adaptor.out.9 diff --git a/bp_test/in/clip_adaptor.in b/bp_test/in/clip_adaptor.in index dd0bce5..e8e5b8e 100644 --- a/bp_test/in/clip_adaptor.in +++ b/bp_test/in/clip_adaptor.in @@ -1,8 +1,27 @@ -SEQ_NAME: 3_XeZ3OvwXsN1/1 -SEQ: CGCGAATCGGACTGGATNTCGCCGCTGACGACCTC -SEQ_LEN: 35 -SCORES: a`_aa_^````\TY``WDGU[BBBBBBBBBBBBBB -ADAPTOR_POS: 26 -ADAPTOR_LEN: 9 -ADAPTOR_MATCH: GACGACCTC +SEQ_NAME: test +SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG +SEQ_LEN: 82 +SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 10 +ADAPTOR_PAT_LEFT: gatcgatcgt +--- +SEQ_NAME: test +SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG +SEQ_LEN: 82 +SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh +ADAPTOR_POS_RIGHT: 72 +ADAPTOR_LEN_RIGHT: 10 +ADAPTOR_PAT_RIGHT: tgctagctag +--- +SEQ_NAME: test +SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG +SEQ_LEN: 82 +SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 10 +ADAPTOR_PAT_LEFT: gatcgatcgt +ADAPTOR_POS_RIGHT: 72 +ADAPTOR_LEN_RIGHT: 10 +ADAPTOR_PAT_RIGHT: tgctagctag --- diff --git a/bp_test/in/find_adaptor.in b/bp_test/in/find_adaptor.in index 8bf5394..8454bfa 100644 --- a/bp_test/in/find_adaptor.in +++ b/bp_test/in/find_adaptor.in @@ -1,32 +1,88 @@ -SEQ_NAME: test_full_length_adaptor -SEQ: TCGTATGCCGTCTTCTGCTTG -SEQ_LEN: 21 +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 --- -SEQ_NAME: test_begin_match -SEQ: TCGTATGCCGTCTTCTGCTTGactacgt -SEQ_LEN: 28 +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 --- -SEQ_NAME: test_middle_match -SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt -SEQ_LEN: 37 +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 --- -SEQ_NAME: test_end_match -SEQ: gactgaTCGTATGCCGTCTTCTGCTTG +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt SEQ_LEN: 27 --- -SEQ_NAME: test_end_trim -SEQ: gtgacactatcgatacgatcgacactgaTCGTA -SEQ_LEN: 33 +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 --- -SEQ_NAME: test_mismatches -SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt -SEQ_LEN: 37 +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 --- -SEQ_NAME: test_insertions -SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt -SEQ_LEN: 37 +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 --- -SEQ_NAME: test_deletions -SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt -SEQ_LEN: 37 +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 --- diff --git a/bp_test/out/clip_adaptor.out.1 b/bp_test/out/clip_adaptor.out.1 index 464527d..1a03457 100644 --- a/bp_test/out/clip_adaptor.out.1 +++ b/bp_test/out/clip_adaptor.out.1 @@ -1,8 +1,27 @@ -SEQ_NAME: 3_XeZ3OvwXsN1/1 -SEQ: CGCGAATCGGACTGGATNTCGCCGCT -SEQ_LEN: 26 -SCORES: a`_aa_^````\TY``WDGU[BBBBB -ADAPTOR_POS: 26 -ADAPTOR_LEN: 9 -ADAPTOR_MATCH: GACGACCTC +SEQ_NAME: test +SEQ: acgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG +SEQ_LEN: 72 +SCORES: JKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 10 +ADAPTOR_PAT_LEFT: gatcgatcgt +--- +SEQ_NAME: test +SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagca +SEQ_LEN: 72 +SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJ +ADAPTOR_POS_RIGHT: 72 +ADAPTOR_LEN_RIGHT: 10 +ADAPTOR_PAT_RIGHT: tgctagctag +--- +SEQ_NAME: test +SEQ: acgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagca +SEQ_LEN: 62 +SCORES: JKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJ +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 10 +ADAPTOR_PAT_LEFT: gatcgatcgt +ADAPTOR_POS_RIGHT: 72 +ADAPTOR_LEN_RIGHT: 10 +ADAPTOR_PAT_RIGHT: tgctagctag --- diff --git a/bp_test/out/find_adaptor.out.1 b/bp_test/out/find_adaptor.out.1 index f59114e..eb723c9 100644 --- a/bp_test/out/find_adaptor.out.1 +++ b/bp_test/out/find_adaptor.out.1 @@ -1,40 +1,106 @@ -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: 0 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_middle_match -SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt -SEQ_LEN: 37 -ADAPTOR_POS: 9 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_end_match -SEQ: gactgaTCGTATGCCGTCTTCTGCTTG +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 6 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt SEQ_LEN: 27 -ADAPTOR_POS: 6 -ADAPTOR_LEN: 21 --- -SEQ_NAME: test_end_trim -SEQ: gtgacactatcgatacgatcgacactgaTCGTA -SEQ_LEN: 33 +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT --- -SEQ_NAME: test_mismatches -SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt -SEQ_LEN: 37 +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 --- -SEQ_NAME: test_insertions -SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt -SEQ_LEN: 37 +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 --- -SEQ_NAME: test_deletions -SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt -SEQ_LEN: 37 +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 --- diff --git a/bp_test/out/find_adaptor.out.10 b/bp_test/out/find_adaptor.out.10 new file mode 100644 index 0000000..f7f0b15 --- /dev/null +++ b/bp_test/out/find_adaptor.out.10 @@ -0,0 +1,130 @@ +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 7 +ADAPTOR_LEN_LEFT: 22 +ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 4 +ADAPTOR_LEN_LEFT: 22 +ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 7 +ADAPTOR_LEN_RIGHT: 22 +ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 4 +ADAPTOR_LEN_RIGHT: 22 +ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 7 +ADAPTOR_LEN_LEFT: 22 +ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 43 +ADAPTOR_LEN_RIGHT: 22 +ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +ADAPTOR_POS_RIGHT: 25 +ADAPTOR_LEN_RIGHT: 22 +ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +ADAPTOR_POS_LEFT: 7 +ADAPTOR_LEN_LEFT: 22 +ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 22 +ADAPTOR_PAT_LEFT: TCGTATGaaCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 47 +ADAPTOR_LEN_RIGHT: 22 +ADAPTOR_PAT_RIGHT: TGACTACGACTAaaCGACTACT +--- diff --git a/bp_test/out/find_adaptor.out.2 b/bp_test/out/find_adaptor.out.2 index c5eb741..3bfeedc 100644 --- a/bp_test/out/find_adaptor.out.2 +++ b/bp_test/out/find_adaptor.out.2 @@ -1,42 +1,100 @@ -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: 0 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_middle_match -SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt -SEQ_LEN: 37 -ADAPTOR_POS: 9 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_end_match -SEQ: gactgaTCGTATGCCGTCTTCTGCTTG +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 6 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt SEQ_LEN: 27 -ADAPTOR_POS: 6 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_end_trim -SEQ: gtgacactatcgatacgatcgacactgaTCGTA -SEQ_LEN: 33 -ADAPTOR_POS: 28 -ADAPTOR_LEN: 5 ---- -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 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 --- diff --git a/bp_test/out/find_adaptor.out.3 b/bp_test/out/find_adaptor.out.3 index 029538b..1e7ac79 100644 --- a/bp_test/out/find_adaptor.out.3 +++ b/bp_test/out/find_adaptor.out.3 @@ -1,42 +1,106 @@ -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: 0 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_middle_match -SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt -SEQ_LEN: 37 -ADAPTOR_POS: 9 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_end_match -SEQ: gactgaTCGTATGCCGTCTTCTGCTTG +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 9 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 6 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt SEQ_LEN: 27 -ADAPTOR_POS: 6 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_end_trim -SEQ: gtgacactatcgatacgatcgacactgaTCGTA -SEQ_LEN: 33 ---- -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 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +ADAPTOR_POS_RIGHT: 27 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 --- diff --git a/bp_test/out/find_adaptor.out.4 b/bp_test/out/find_adaptor.out.4 index 8da18a4..23667bb 100644 --- a/bp_test/out/find_adaptor.out.4 +++ b/bp_test/out/find_adaptor.out.4 @@ -1,42 +1,100 @@ -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: 0 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_middle_match -SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt -SEQ_LEN: 37 -ADAPTOR_POS: 9 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_end_match -SEQ: gactgaTCGTATGCCGTCTTCTGCTTG +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt SEQ_LEN: 27 -ADAPTOR_POS: 6 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_end_trim -SEQ: gtgacactatcgatacgatcgacactgaTCGTA -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 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 9 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 6 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 --- diff --git a/bp_test/out/find_adaptor.out.5 b/bp_test/out/find_adaptor.out.5 index a337be4..c9f66db 100644 --- a/bp_test/out/find_adaptor.out.5 +++ b/bp_test/out/find_adaptor.out.5 @@ -1,42 +1,124 @@ -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: 0 -ADAPTOR_LEN: 21 ---- -SEQ_NAME: test_middle_match -SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt -SEQ_LEN: 37 -ADAPTOR_POS: 7 -ADAPTOR_LEN: 23 ---- -SEQ_NAME: test_end_match -SEQ: gactgaTCGTATGCCGTCTTCTGCTTG +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 6 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 9 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 6 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt SEQ_LEN: 27 -ADAPTOR_POS: 4 -ADAPTOR_LEN: 23 ---- -SEQ_NAME: test_end_trim -SEQ: gtgacactatcgatacgatcgacactgaTCGTA -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 -ADAPTOR_POS: 9 -ADAPTOR_LEN: 23 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +ADAPTOR_POS_RIGHT: 27 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 --- diff --git a/bp_test/out/find_adaptor.out.6 b/bp_test/out/find_adaptor.out.6 new file mode 100644 index 0000000..5593ea1 --- /dev/null +++ b/bp_test/out/find_adaptor.out.6 @@ -0,0 +1,133 @@ +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 6 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 1 +ADAPTOR_PAT_LEFT: T +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 1 +ADAPTOR_PAT_LEFT: T +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 9 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 6 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 11 +ADAPTOR_PAT_LEFT: GTCTTCTGCTT +ADAPTOR_POS_RIGHT: 27 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 +--- diff --git a/bp_test/out/find_adaptor.out.7 b/bp_test/out/find_adaptor.out.7 new file mode 100644 index 0000000..bbf6ebf --- /dev/null +++ b/bp_test/out/find_adaptor.out.7 @@ -0,0 +1,169 @@ +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 19 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: T +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 26 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 35 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 6 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 25 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: T +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +ADAPTOR_POS_RIGHT: 26 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 35 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 1 +ADAPTOR_PAT_LEFT: T +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 1 +ADAPTOR_PAT_LEFT: T +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 9 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 6 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 27 +ADAPTOR_POS_RIGHT: 26 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 35 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 11 +ADAPTOR_PAT_LEFT: GTCTTCTGCTT +ADAPTOR_POS_RIGHT: 27 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 10 +ADAPTOR_PAT_RIGHT: TGACTACGAC +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_RIGHT: 71 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +ADAPTOR_POS_RIGHT: 67 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 +ADAPTOR_POS_RIGHT: 75 +ADAPTOR_LEN_RIGHT: 1 +ADAPTOR_PAT_RIGHT: t +--- diff --git a/bp_test/out/find_adaptor.out.8 b/bp_test/out/find_adaptor.out.8 new file mode 100644 index 0000000..1d7adab --- /dev/null +++ b/bp_test/out/find_adaptor.out.8 @@ -0,0 +1,130 @@ +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 6 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 9 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 6 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +ADAPTOR_POS_RIGHT: 27 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTAccCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGAggACGACTACT +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 +--- diff --git a/bp_test/out/find_adaptor.out.9 b/bp_test/out/find_adaptor.out.9 new file mode 100644 index 0000000..50442b8 --- /dev/null +++ b/bp_test/out/find_adaptor.out.9 @@ -0,0 +1,130 @@ +SEQ_NAME: test_full_length_match_forward +SEQ: TCGTATGCCGTCTTCTGCTT +SEQ_LEN: 20 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_begin_match_forward +SEQ: TCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_LEFT: 0 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_middle_match_forward +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_end_match_forward +SEQ: gactgaTCGTATGCCGTCTTCTGCTT +SEQ_LEN: 26 +ADAPTOR_POS_LEFT: 6 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_full_length_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_forward_rc +SEQ: AAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_forward_rc +SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_forward_rc +SEQ: gactgaAAGCAGAAGACGGCATACGA +SEQ_LEN: 26 +--- +SEQ_NAME: test_full_length_match_reverse +SEQ: TGACTACGACTACGACTACT +SEQ_LEN: 20 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_begin_match_reverse +SEQ: TGACTACGACTACGACTACTactacgt +SEQ_LEN: 27 +ADAPTOR_POS_RIGHT: 0 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_middle_match_reverse +SEQ: actgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 36 +ADAPTOR_POS_RIGHT: 9 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_end_match_reverse +SEQ: gactgaTGACTACGACTACGACTACT +SEQ_LEN: 26 +ADAPTOR_POS_RIGHT: 6 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_full_length_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 20 +--- +SEQ_NAME: test_begin_match_reverse_rc +SEQ: AGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 27 +--- +SEQ_NAME: test_middle_match_reverse_rc +SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt +SEQ_LEN: 36 +--- +SEQ_NAME: test_end_match_reverse_rc +SEQ: gactgaAGTAGTCGTAGTCGTAGTCA +SEQ_LEN: 26 +--- +SEQ_NAME: test_forward_and_reverse_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 72 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 45 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_forward_partial_match +SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt +SEQ_LEN: 54 +ADAPTOR_POS_RIGHT: 27 +ADAPTOR_LEN_RIGHT: 20 +ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT +--- +SEQ_NAME: test_reverse_partial_match +SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC +SEQ_LEN: 55 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 20 +ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT +--- +SEQ_NAME: test_forward_and_reverse_match_with_mismatch +SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt +SEQ_LEN: 72 +--- +SEQ_NAME: test_forward_and_reverse_match_with_insertion +SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt +SEQ_LEN: 68 +ADAPTOR_POS_LEFT: 9 +ADAPTOR_LEN_LEFT: 18 +ADAPTOR_PAT_LEFT: TCGTATCGTCTTCTGCTT +ADAPTOR_POS_RIGHT: 43 +ADAPTOR_LEN_RIGHT: 18 +ADAPTOR_PAT_RIGHT: TGACTACGACCGACTACT +--- +SEQ_NAME: test_forward_and_reverse_match_with_deletion +SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt +SEQ_LEN: 76 +--- diff --git a/bp_test/test/test_find_adaptor b/bp_test/test/test_find_adaptor index cbbe4a7..19f68fd 100755 --- a/bp_test/test/test_find_adaptor +++ b/bp_test/test/test_find_adaptor @@ -2,22 +2,42 @@ source "$BP_DIR/bp_test/lib/test.sh" -run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 0 -I $in -O $tmp" +run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -I $in -O $tmp" assert_no_diff $tmp $out.1 clean -run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 0 -p -l 5 -I $in -O $tmp" +run "$bp -m 0 -i 0 -d 0 -F TCGTATGCCGTCTTCTGCTT -I $in -O $tmp" assert_no_diff $tmp $out.2 clean -run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 10 -i 0 -d 0 -I $in -O $tmp" +run "$bp -m 0 -i 0 -d 0 -r TGACTACGACTACGACTACT -I $in -O $tmp" assert_no_diff $tmp $out.3 clean -run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 10 -d 0 -I $in -O $tmp" +run "$bp -m 0 -i 0 -d 0 -R TGACTACGACTACGACTACT -I $in -O $tmp" assert_no_diff $tmp $out.4 clean -run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 10 -I $in -O $tmp" +run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp" assert_no_diff $tmp $out.5 clean + +run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -I $in -O $tmp" +assert_no_diff $tmp $out.6 +clean + +run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -L 1 -I $in -O $tmp" +assert_no_diff $tmp $out.7 +clean + +run "$bp -m 10 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp" +assert_no_diff $tmp $out.8 +clean + +run "$bp -m 0 -i 10 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp" +assert_no_diff $tmp $out.9 +clean + +run "$bp -m 0 -i 0 -d 10 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp" +assert_no_diff $tmp $out.10 +clean -- 2.39.5