| Previous changeset 6:fd05b142b3a3 (2024-08-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278 |
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modified:
macros.xml test-data/meme_output_test1.html test-data/meme_output_test1.txt test-data/meme_output_test1.xml test-data/meme_output_test2.html test-data/meme_output_test2.txt test-data/meme_output_test2.xml |
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added:
test-data/alphabet.txt test-data/meme_input_m.fasta test-data/meme_output_custom.html test-data/meme_output_custom.txt test-data/meme_output_custom.xml test-data/streme_input_neg2.fasta test-data/streme_input_pos.fasta test-data/streme_input_pos2.fasta test-data/streme_output_test1.html test-data/streme_output_test1.txt test-data/streme_output_test1.xml test-data/streme_output_test2.html test-data/streme_output_test2.txt test-data/streme_output_test2.xml test-data/streme_output_test3.html test-data/streme_output_test3.txt test-data/streme_output_test3.xml |
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| diff -r fd05b142b3a3 -r 0c97e5c18468 macros.xml --- a/macros.xml Thu Aug 29 10:19:55 2024 +0000 +++ b/macros.xml Mon Jul 14 21:33:41 2025 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">5.5.6</token> + <token name="@TOOL_VERSION@">5.5.8</token> <token name="@PROFILE@">23.0</token> <xml name="requirements"> <requirements> |
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| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/alphabet.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alphabet.txt Mon Jul 14 21:33:41 2025 +0000 |
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| @@ -0,0 +1,13 @@ +ALPHABET "DNA with covalent modifications" DNA-LIKE + +# Core uppercase symbols +A "Adenine" 8510A8 ~ T "Thymine" A89610 +C "Cytosine" A50026 ~ G "Guanine" 313695 + +# Covalent modifications +m "5-Methylcytosine" D73027 ~ 1 "Guanine:5-Methylcytosine" 4575B4 +h "5-Hydroxymethylcytosine" F46D43 ~ 2 "Guanine:5-Hydroxymethylcytosine" 74ADD1 +f "5-Formylcytosine" FDAE61 ~ 3 "Guanine:5-Formylcytosine" ABD9E9 +c "5-Carboxylcytosine" FEE090 ~ 4 "Guanine:5-Carboxylcytosine" E0F3F8 +a "N6-methyladenine" 8510A8 ~ t "Thymine_lowercase" 756BB1 +g "modified_g" 00897B ~ 5 "cytosine_lowercase" 53698A |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_input_m.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_input_m.fasta Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,66 @@ +>chr21_19617074_19617124_+ +AAAAATTATTACTAGGGAGGGGGCCGGAACCTCGGGACGTGGGTATATAA +>chr21_26934381_26934431_+ +GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT +>chr21_28217753_28217803_- +CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTmCACTATAAA +>chr21_31710037_31710087_- +AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT +>chr21_31744582_31744632_- +CCmAGGTCTAAGAGCATATATAACTTGGAGTCCAGACTATGACATTCAAA +>chr21_31768316_31768366_+ +AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAAACTmAGAATCTT +>chr21_31914206_31914256_- +TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGACACC +>chr21_31933633_31933683_- +TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAAACTGACCT +>chr21_31962741_31962791_- +ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGGAGAGTCAA +>chr21_31964683_31964733_+ +TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTGTCCATAC +>chr21_31973364_31973414_+ +aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC +>chr21_31992870_31992920_+ +CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT +>chr21_32185595_32185645_- +TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA +>chr21_32202076_32202126_- +TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT +>chr21_32253899_32253949_- +AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC +>chr21_32410820_32410870_- +TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG +>chr21_36411748_36411798_- +ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt +>chr21_37838750_37838800_- +gatggttttataaggggcctcaccctcggctcagccctcattcttctcct +>chr21_45705687_45705737_+ +CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGGGTATAACAGC +>chr21_45971413_45971463_- +CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca +>chr21_45978668_45978718_- +CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca +>chr21_45993530_45993580_+ +CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCACTCGC +>chr21_46020421_46020471_+ +GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc +>chr21_46031920_46031970_+ +GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC +>chr21_46046964_46047014_+ +ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca +>chr21_46057197_46057247_+ +ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC +>chr21_46086869_46086919_- +GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC +>chr21_46102103_46102153_- +AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGmGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGmTGCCGGTGAGCGTATAAAGGCCCTGGCG +>chr21_47575506_47575556_- +TGAGAAGCmGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG |
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| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_custom.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_custom.html Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| b'@@ -0,0 +1,276 @@\n+ "options": {\n+ "mod": "zoops",\n+ "revcomp": false,\n+ "nmotifs": 1,\n+ "objfun": "E-value of product of p-values",\n+ "spfun": "E-value of product of p-values",\n+ "minw": 8,\n+ "maxw": 50,\n+ "minsites": 2,\n+ "maxsites": 30,\n+ "wnsites": 0.8,\n+ "spmap": "uni",\n+ "spfuzz": 0.5,\n+ "searchsize": 1500,\n+ "maxsize": 1000000,\n+ "norand": "no",\n+ "csites": 1000,\n+ "hsfrac": 0,\n+ "prior": "dirichlet",\n+ "b": 0.01,\n+ "maxiter": 50,\n+ "distance": 0.001,\n+ "wg": 11,\n+ "ws": 1,\n+ "noendgaps": false,\n+ "substring": true,\n+ "seed": 0,\n+ "brief": 1000\n+ },\n+ "alphabet": {\n+ "name": "DNA with covalent modifications",\n+ "like": "dna",\n+ "ncore": 16,\n+ "symbols": [\n+ {\n+ "symbol": "A",\n+ "name": "Adenine",\n+ "colour": "8510A8",\n+ "complement": "T"\n+ }, {\n+ "symbol": "C",\n+ "name": "Cytosine",\n+ "colour": "A50026",\n+ "complement": "G"\n+ }, {\n+ "symbol": "G",\n+ "name": "Guanine",\n+ "colour": "313695",\n+ "complement": "C"\n+ }, {\n+ "symbol": "T",\n+ "name": "Thymine",\n+ "colour": "A89610",\n+ "complement": "A"\n+ }, {\n+ "symbol": "a",\n+ "name": "N6-methyladenine",\n+ "colour": "8510A8",\n+ "complement": "t"\n+ }, {\n+ "symbol": "c",\n+ "name": "5-Carboxylcytosine",\n+ "colour": "FEE090",\n+ "complement": "4"\n+ }, {\n+ "symbol": "f",\n+ "name": "5-Formylcytosine",\n+ "colour": "FDAE61",\n+ "complement": "3"\n+ }, {\n+ "symbol": "g",\n+ "name": "modified_g",\n+ "colour": "00897B",\n+ "complement": "5"\n+ }, {\n+ "symbol": "h",\n+ "name": "5-Hydroxymethylcytosine",\n+ "colour": "F46D43",\n+ "complement": "2"\n+ }, {\n+ "symbol": "m",\n+ "name": "5-Methylcytosine",\n+ "colour": "D73027",\n+ "complement": "1"\n+ }, {\n+ "symbol": "t",\n+ "name": "Thymine_lowercase",\n+ "colour": "756BB1",\n+ "complement": "a"\n+ }, {\n+ "symbol": "1",\n+ "name": "Guanine:5-Methylcytosine",\n+ "colour": "4575B4",\n+ "complement": "m"\n+ }, {\n+ "symbol": "2",\n+ "name": "Guanine:5-Hydroxymethylcytosine",\n+ "colour": "74ADD1",\n+ "complement": "h"\n+ }, {\n+ "symbol": "3",\n+ "name": "Guanine:5-Formylcytosine",\n+ "colour": "ABD9E9",\n+ "complement": "f"\n+ }, {\n+ "symbol": "4",\n+ "name": "Guanine:5-Carboxylcytosine",\n+ "colour": "E0F3F8",\n+ "complement": "c"\n+ }, {\n+ "symbol": "5",\n+ "name": "cytosine_lowercase",\n+ "colour": "53698A",\n+ "complement": "g"\n+ }, {\n+ "symbol": "?",\n+ "equals": "ACGTacfghmt12345"\n+ }\n+ ]\n+ },\n+ "background": {\n+ "source": "--sequences--",\n+ "order": 0,\n+ "freqs": [\n+ 0.263, 0.2, 0.249, 0.189, 0.0297, 0.027, 0.00066, 0.00726,\n+ 0.00066, 0.00396, 0.0277, 0.00066, 0.00066, 0.00066, 0.00066,\n+ 0.00066\n+ ]\n+ },\n+ "sequence_db": {\n+ "prim'..b' "weight": 1.000000\n+ }, {\n+ "name": "chr21_31710037_31710087_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31744582_31744632_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31768316_31768366_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31914206_31914256_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31933633_31933683_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31962741_31962791_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31964683_31964733_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31973364_31973414_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_31992870_31992920_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_32185595_32185645_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_32202076_32202126_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_32253899_32253949_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_32410820_32410870_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_36411748_36411798_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_37838750_37838800_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_45705687_45705737_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_45971413_45971463_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_45978668_45978718_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_45993530_45993580_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_46020421_46020471_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_46031920_46031970_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_46046964_46047014_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_46057197_46057247_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_46086869_46086919_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_46102103_46102153_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_47517957_47518007_+",\n+ "length": 50,\n+ "weight": 1.000000\n+ }, {\n+ "name": "chr21_47575506_47575556_-",\n+ "length": 50,\n+ "weight": 1.000000\n+ }\n+ ]\n+ },\n+ "motifs": [\n+ {\n+ "db": 0,\n+ "id": "taCaaACAGtataactctcac",\n+ "alt": "MEME-1",\n+ "len": 21,\n+ "nsites": 5,\n+ "evalue": "4.6e-028",\n+ "ic": 55.7,\n+ "re": 68.0,\n+ "llr": 236,\n+ "bt": 7.73664,\n\\ No newline at end of file\n' |
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| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_custom.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_custom.txt Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,61 @@ +******************************************************************************** +MEME - Motif discovery tool +******************************************************************************** +MEME version 5.5.8 (Release date: Thu May 15 15:01:46 2025 -0700) + +For further information on how to interpret these results please access https://meme-suite.org/meme. +To get a copy of the MEME Suite software please access https://meme-suite.org. + +******************************************************************************** + + +******************************************************************************** +REFERENCE +******************************************************************************** +If you use this program in your research, please cite: + +Timothy L. Bailey and Charles Elkan, +"Fitting a mixture model by expectation maximization to +discover motifs in biopolymers", +Proceedings of the Second International Conference on Intelligent Systems +for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. +******************************************************************************** + + +******************************************************************************** +ALPHABET "DNA with covalent modifications" DNA-LIKE +******************************************************************************** +A "Adenine" 8510A8 ~ T "Thymine" A89610 +C "Cytosine" A50026 ~ G "Guanine" 313695 +a "N6-methyladenine" 8510A8 ~ t "Thymine_lowercase" 756BB1 +c "5-Carboxylcytosine" FEE090 ~ 4 "Guanine:5-Carboxylcytosine" E0F3F8 +f "5-Formylcytosine" FDAE61 ~ 3 "Guanine:5-Formylcytosine" ABD9E9 +g "modified_g" 00897B ~ 5 "cytosine_lowercase" 53698A +h "5-Hydroxymethylcytosine" F46D43 ~ 2 "Guanine:5-Hydroxymethylcytosine" 74ADD1 +m "5-Methylcytosine" D73027 ~ 1 "Guanine:5-Methylcytosine" 4575B4 +? = ACGTacfghmt12345 +******************************************************************************** + +******************************************************************************** +TRAINING SET +******************************************************************************** +PRIMARY SEQUENCES= Galaxy_FASTA_Input +CONTROL SEQUENCES= --none-- +Sequence name Weight Length Sequence name Weight Length +------------- ------ ------ ------------- ------ ------ +chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 +chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 +chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 +chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 +chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 +chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 +chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 +chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 +chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 +chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 +chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 +chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 +chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 +chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 +chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 +******************************************************************************** \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_custom.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_custom.xml Mon Jul 14 21:33:41 2025 +0000 |
| b |
| b'@@ -0,0 +1,946 @@\n+<alphabet_matrix>\n+<alphabet_array>\n+<value letter_id="A">61</value>\n+<value letter_id="C">-897</value>\n+<value letter_id="G">-897</value>\n+<value letter_id="T">-897</value>\n+<value letter_id="a">-897</value>\n+<value letter_id="c">-897</value>\n+<value letter_id="f">-897</value>\n+<value letter_id="g">-897</value>\n+<value letter_id="h">-897</value>\n+<value letter_id="m">-897</value>\n+<value letter_id="t">443</value>\n+<value letter_id="n1">-897</value>\n+<value letter_id="n2">-897</value>\n+<value letter_id="n3">-897</value>\n+<value letter_id="n4">-897</value>\n+<value letter_id="n5">-897</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-897</value>\n+<value letter_id="C">0</value>\n+<value letter_id="G">-31</value>\n+<value letter_id="T">-897</value>\n+<value letter_id="a">375</value>\n+<value letter_id="c">-897</value>\n+<value letter_id="f">-897</value>\n+<value letter_id="g">-897</value>\n+<value letter_id="h">-897</value>\n+<value letter_id="m">-897</value>\n+<value letter_id="t">285</value>\n+<value letter_id="n1">-897</value>\n+<value letter_id="n2">-897</value>\n+<value letter_id="n3">-897</value>\n+<value letter_id="n4">-897</value>\n+<value letter_id="n5">-897</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-897</value>\n+<value letter_id="C">100</value>\n+<value letter_id="G">-897</value>\n+<value letter_id="T">-897</value>\n+<value letter_id="a">375</value>\n+<value letter_id="c">-897</value>\n+<value letter_id="f">-897</value>\n+<value letter_id="g">-897</value>\n+<value letter_id="h">-897</value>\n+<value letter_id="m">-897</value>\n+<value letter_id="t">285</value>\n+<value letter_id="n1">-897</value>\n+<value letter_id="n2">-897</value>\n+<value letter_id="n3">-897</value>\n+<value letter_id="n4">-897</value>\n+<value letter_id="n5">-897</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-897</value>\n+<value letter_id="C">0</value>\n+<value letter_id="G">-897</value>\n+<value letter_id="T">8</value>\n+<value letter_id="a">433</value>\n+<value letter_id="c">-897</value>\n+<value letter_id="f">-897</value>\n+<value letter_id="g">-897</value>\n+<value letter_id="h">-897</value>\n+<value letter_id="m">-897</value>\n+<value letter_id="t">-897</value>\n+<value letter_id="n1">-897</value>\n+<value letter_id="n2">-897</value>\n+<value letter_id="n3">-897</value>\n+<value letter_id="n4">-897</value>\n+<value letter_id="n5">-897</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">61</value>\n+<value letter_id="C">-897</value>\n+<value letter_id="G">-897</value>\n+<value letter_id="T">-897</value>\n+<value letter_id="a">433</value>\n+<value letter_id="c">-897</value>\n+<value letter_id="f">-897</value>\n+<value letter_id="g">-897</value>\n+<value letter_id="h">-897</value>\n+<value letter_id="m">-897</value>\n+<value letter_id="t">-897</value>\n+<value letter_id="n1">-897</value>\n+<value letter_id="n2">-897</value>\n+<value letter_id="n3">-897</value>\n+<value letter_id="n4">-897</value>\n+<value letter_id="n5">-897</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">61</value>\n+<value letter_id="C">-897</value>\n+<value letter_id="G">-897</value>\n+<value letter_id="T">-897</value>\n+<value letter_id="a">375</value>\n+<value letter_id="c">-897</value>\n+<value letter_id="f">-897</value>\n+<value letter_id="g">478</value>\n+<value letter_id="h">-897</value>\n+<value letter_id="m">-897</value>\n+<value letter_id="t">-897</value>\n+<value letter_id="n1">-897</value>\n+<value letter_id="n2">-897</value>\n+<value letter_id="n3">-897</value>\n+<value letter_id="n4">-897</value>\n+<value letter_id="n5">-897</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-897</value>\n+<value letter_id="C">100</value>\n+<value letter_id="G">-897</value>\n+<value letter_id="T">-897</value>\n+<value letter_id="a">-897</value>\n+<value letter_id="c">288</value>\n+<value letter_id="f">-897</value>\n+<value letter_id="g">478</value>\n+<value letter_id="h">-897</value>\n+<value letter_id="m">-897</value>\n+<value let'..b'd="A"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="a"/>\n+<letter_ref letter_id="c"/>\n+<letter_ref letter_id="t"/>\n+<letter_ref letter_id="c"/>\n+<letter_ref letter_id="a"/>\n+<letter_ref letter_id="c"/>\n+<letter_ref letter_id="t"/>\n+<letter_ref letter_id="c"/>\n+</site>\n+<right_flank></right_flank>\n+</contributing_site>\n+</contributing_sites>\n+</motif>\n+</motifs>\n+<scanned_sites_summary p_thresh="0.0001">\n+<scanned_sites sequence_id="sequence_0" pvalue="9.99e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_1" pvalue="9.78e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_2" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_3" pvalue="9.99e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_4" pvalue="9.99e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_5" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_6" pvalue="9.61e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_7" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_8" pvalue="9.65e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_9" pvalue="9.67e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_10" pvalue="6.20e-25" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="2.07e-26"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_11" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_12" pvalue="7.25e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_13" pvalue="9.59e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_14" pvalue="7.20e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_15" pvalue="9.99e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_16" pvalue="2.29e-26" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="28" pvalue="7.62e-28"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_17" pvalue="3.02e-32" num_sites="2"><scanned_site motif_id="motif_1" strand="plus" position="8" pvalue="1.01e-33"/>\n+<scanned_site motif_id="motif_1" strand="plus" position="29" pvalue="1.08e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_18" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_19" pvalue="2.46e-16" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="28" pvalue="8.19e-18"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_20" pvalue="1.27e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="28" pvalue="4.22e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_21" pvalue="9.58e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_22" pvalue="2.70e-14" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="29" pvalue="9.00e-16"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_23" pvalue="9.69e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_24" pvalue="2.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="28" pvalue="8.43e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_25" pvalue="9.67e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_26" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_27" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_28" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_29" pvalue="1.00e+00" num_sites="0"></scanned_sites>\n+</scanned_sites_summary>\n+</MEME>\n' |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_test1.html --- a/test-data/meme_output_test1.html Thu Aug 29 10:19:55 2024 +0000 +++ b/test-data/meme_output_test1.html Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| @@ -1,73 +1,124 @@ - <script> - { - $("opt_mod").className = data.options.mod; - $("opt_objfun").textContent = data.options.objfun; - $("opt_spfun").textContent = data.options.spfun; - $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none"); - $("opt_nmotifs").textContent = data.options.nmotifs; - $("opt_evt").textContent = (typeof data.options.evt === "number" ? data.options.evt : "no limit"); - $("opt_minw").textContent = data.options.minw; - $("opt_maxw").textContent = data.options.maxw; - $("opt_minsites").textContent = data.options.minsites; - $("opt_maxsites").textContent = data.options.maxsites; - $("opt_wnsites").textContent = data.options.wnsites; - $("opt_spmap").className = data.options.spmap; - $("opt_spfuzz").textContent = data.options.spfuzz; - $("opt_prior").className = data.options.prior; - if (data.options.prior == "dirichlet") { - $("opt_prior_source").textContent = make_background_source("Source", data.background.source, true); - } else { - $("opt_prior_source").textContent = (data.options.prior == "addone") ? "motif observed frequencies" : data.options.priors_source; - } - $("opt_b").textContent = (data.options.b < 0) ? "not applicable" : (data.options.b == 0) ? "intrinsic strength" : data.options.b; - $("opt_maxiter").textContent = data.options.maxiter; - $("opt_distance").textContent = data.options.distance; - $("opt_searchsize").textContent = data.options.searchsize; - if (typeof data.options.csites != "undefined") { - $("opt_csites").textContent = data.options.csites; - } else { - $("opt_csites").parentElement.style.display = "none" - } - if (typeof data.options.wg != "undefined") { - $("opt_wg").textContent = data.options.wg; - } else { - $("opt_wg").parentElement.style.display = "none" - } - if (typeof data.options.ws != "undefined") { - $("opt_ws").textContent = data.options.ws; - } - else { - $("opt_ws").parentElement.style.display = "none" - } - if (typeof data.options.noendgaps != "undefined") { - $("opt_noendgaps").className = (data.options.noendgaps ? "on" : "off"); - } - else { - $("opt_noendgaps").parentElement.style.display = "none" - } - $("opt_substring").className = (data.options.substring ? "on" : "off"); - } - </script> - </div> - <!-- list information on this program --> - <div id="info_sec" class="bar"> - <div class="subsection"> - <h5 id="version">MEME version</h5> - <span id="ins_version"></span> - (Release date: <span id="ins_release"></span>)<br> - </div> - <script> - $("ins_version").innerHTML = data["version"]; - $("ins_release").innerHTML = data["release"]; - </script> - <div class="subsection" id="reference"> <script>print_citation("reference", "MEME");</script></div> - <div class="subsection"> - <h5 id="command">Command line</h5> - <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly"> - </textarea> - <script>$("cmd").value = data["cmd"].join(" ");</script> - </div> - </div> - - </body> -</html> + "sequences": [ + { + "name": "chr21_19617074_19617124_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_26934381_26934431_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_28217753_28217803_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31710037_31710087_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31744582_31744632_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31768316_31768366_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31914206_31914256_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31933633_31933683_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31962741_31962791_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31964683_31964733_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31973364_31973414_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_31992870_31992920_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_32185595_32185645_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_32202076_32202126_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_32253899_32253949_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_32410820_32410870_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_36411748_36411798_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_37838750_37838800_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_45705687_45705737_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_45971413_45971463_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_45978668_45978718_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_45993530_45993580_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_46020421_46020471_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_46031920_46031970_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_46046964_46047014_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_46057197_46057247_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_46086869_46086919_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_46102103_46102153_-", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_47517957_47518007_+", + "length": 50, + "weight": 1.000000 + }, { + "name": "chr21_47575506_47575556_-", + "length": 50, + "weight": 1.000000 + } + ] + }, \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_test1.txt --- a/test-data/meme_output_test1.txt Thu Aug 29 10:19:55 2024 +0000 +++ b/test-data/meme_output_test1.txt Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| b'@@ -1,39 +1,207 @@\n+model: mod= zoops nmotifs= 1 evt= inf\n+objective function: em= E-value of product of p-values\n+ starts= E-value of product of p-values\n+width: minw= 8 maxw= 50\n+nsites: minsites= 2 maxsites= 30 wnsites= 0.8\n+theta: spmap= pam spfuzz= 120\n+em: prior= megap b= 7500 maxiter= 50\n+ distance= 1e-05\n+trim: wg= 11 ws= 1 endgaps= yes\n+data: n= 1500 N= 30\n+sample: seed= 0 hsfrac= 0\n+ searchsize= 1500 norand= no csites= 1000\n+Dirichlet mixture priors file: prior30.plib\n+Letter frequencies in dataset:\n+A 0.294 C 0.231 D 0 E 0 F 0 G 0.257 H 0 I 0 K 0 \n+L 0 M 0 N 0 P 0 Q 0 R 0 S 0 T 0.217 V 0 \n+W 0 Y 0 \n+Background letter frequencies (from file dataset with add-one prior applied):\n+A 0.291 C 0.229 D 0.000658 E 0.000658 F 0.000658 G 0.255 H 0.000658 I 0.000658 K 0.000658 \n+L 0.000658 M 0.000658 N 0.000658 P 0.000658 Q 0.000658 R 0.000658 S 0.000658 T 0.215 V 0.000658 \n+W 0.000658 Y 0.000658 \n+Background model order: 0\n ********************************************************************************\n-SUMMARY OF MOTIFS\n+\n+\n+********************************************************************************\n+MOTIF GGGGTATAAAA MEME-1\twidth = 11 sites = 25 llr = 239 E-value = 2.4e-011\n ********************************************************************************\n+--------------------------------------------------------------------------------\n+\tMotif GGGGTATAAAA MEME-1 Description\n+--------------------------------------------------------------------------------\n+Simplified A 2323:a:a8a8\n+pos.-specific C ::3::::::::\n+probability D :::::::::::\n+matrix E :::::::::::\n+ F :::::::::::\n+ G 7746::::::1\n+ H :::::::::::\n+ I :::::::::::\n+ K :::::::::::\n+ L :::::::::::\n+ M :::::::::::\n+ N :::::::::::\n+ P :::::::::::\n+ Q :::::::::::\n+ R :::::::::::\n+ S :::::::::::\n+ T 1:2:a:a:2::\n+ V :::::::::::\n+ W :::::::::::\n+ Y :::::::::::\n+\n+ bits 10.6 \n+ 9.5 \n+ 8.5 \n+ 7.4 \n+Relative 6.3 \n+Entropy 5.3 \n+(13.8 bits) 4.2 \n+ 3.2 \n+ 2.1 * ** \n+ 1.1 ** ********\n+ 0.0 -----------\n+\n+Multilevel GGGGTATAAAA\n+consensus AACA T \n+sequence \n+ \n+ \n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGGGTATAAAA MEME-1 sites sorted by position p-value\n+--------------------------------------------------------------------------------\n+Sequence name Start P-value Site \n+------------- ----- --------- -----------\n+chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC\n+chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC \n+chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG\n+chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC\n+chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA\n+chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC\n+chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA C'..b' -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 \n+ 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 \n+ -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 \n+ 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 \n+ 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 \n+ 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 \n+ 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 \n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGGGTATAAAA MEME-1 position-specific probability matrix\n+--------------------------------------------------------------------------------\n+letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 \n+ 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000 \n+ 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 \n+ 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000 \n+ 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 \n+ 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000 \n+ 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n+ 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 \n+ 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n+ 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000 \n+ 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n+ 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 \n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGGGTATAAAA MEME-1 regular expression\n+--------------------------------------------------------------------------------\n+[GA][GA][GC][GA]TATA[AT]AA\n+--------------------------------------------------------------------------------\n\\ No newline at end of file\n' |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_test1.xml --- a/test-data/meme_output_test1.xml Thu Aug 29 10:19:55 2024 +0000 +++ b/test-data/meme_output_test1.xml Mon Jul 14 21:33:41 2025 +0000 |
| b |
| b'@@ -1,3 +1,924 @@\n+<alphabet_array>\n+<value letter_id="A">-32</value>\n+<value letter_id="C">-680</value>\n+<value letter_id="D">91</value>\n+<value letter_id="E">77</value>\n+<value letter_id="F">7</value>\n+<value letter_id="G">138</value>\n+<value letter_id="H">-20</value>\n+<value letter_id="I">55</value>\n+<value letter_id="K">64</value>\n+<value letter_id="L">107</value>\n+<value letter_id="M">11</value>\n+<value letter_id="N">150</value>\n+<value letter_id="P">142</value>\n+<value letter_id="Q">72</value>\n+<value letter_id="R">87</value>\n+<value letter_id="S">396</value>\n+<value letter_id="T">-148</value>\n+<value letter_id="V">221</value>\n+<value letter_id="W">-140</value>\n+<value letter_id="Y">-36</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-11</value>\n+<value letter_id="C">-680</value>\n+<value letter_id="D">89</value>\n+<value letter_id="E">76</value>\n+<value letter_id="F">7</value>\n+<value letter_id="G">137</value>\n+<value letter_id="H">-21</value>\n+<value letter_id="I">55</value>\n+<value letter_id="K">63</value>\n+<value letter_id="L">107</value>\n+<value letter_id="M">10</value>\n+<value letter_id="N">149</value>\n+<value letter_id="P">141</value>\n+<value letter_id="Q">71</value>\n+<value letter_id="R">87</value>\n+<value letter_id="S">396</value>\n+<value letter_id="T">-239</value>\n+<value letter_id="V">220</value>\n+<value letter_id="W">-140</value>\n+<value letter_id="Y">-36</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-79</value>\n+<value letter_id="C">41</value>\n+<value letter_id="D">4</value>\n+<value letter_id="E">21</value>\n+<value letter_id="F">-7</value>\n+<value letter_id="G">44</value>\n+<value letter_id="H">-62</value>\n+<value letter_id="I">42</value>\n+<value letter_id="K">-5</value>\n+<value letter_id="L">99</value>\n+<value letter_id="M">0</value>\n+<value letter_id="N">99</value>\n+<value letter_id="P">138</value>\n+<value letter_id="Q">52</value>\n+<value letter_id="R">42</value>\n+<value letter_id="S">399</value>\n+<value letter_id="T">-46</value>\n+<value letter_id="V">223</value>\n+<value letter_id="W">-173</value>\n+<value letter_id="Y">-68</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">11</value>\n+<value letter_id="C">-677</value>\n+<value letter_id="D">48</value>\n+<value letter_id="E">47</value>\n+<value letter_id="F">-2</value>\n+<value letter_id="G">127</value>\n+<value letter_id="H">-43</value>\n+<value letter_id="I">46</value>\n+<value letter_id="K">27</value>\n+<value letter_id="L">101</value>\n+<value letter_id="M">3</value>\n+<value letter_id="N">124</value>\n+<value letter_id="P">138</value>\n+<value letter_id="Q">60</value>\n+<value letter_id="R">62</value>\n+<value letter_id="S">397</value>\n+<value letter_id="T">-235</value>\n+<value letter_id="V">220</value>\n+<value letter_id="W">-160</value>\n+<value letter_id="Y">-55</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-596</value>\n+<value letter_id="C">-820</value>\n+<value letter_id="D">12</value>\n+<value letter_id="E">-21</value>\n+<value letter_id="F">-53</value>\n+<value letter_id="G">-267</value>\n+<value letter_id="H">-74</value>\n+<value letter_id="I">37</value>\n+<value letter_id="K">16</value>\n+<value letter_id="L">44</value>\n+<value letter_id="M">-37</value>\n+<value letter_id="N">98</value>\n+<value letter_id="P">31</value>\n+<value letter_id="Q">9</value>\n+<value letter_id="R">19</value>\n+<value letter_id="S">319</value>\n+<value letter_id="T">212</value>\n+<value letter_id="V">127</value>\n+<value letter_id="W">-193</value>\n+<value letter_id="Y">-95</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">165</value>\n+<value letter_id="C">-261</value>\n+<value letter_id="D">70</value>\n+<value letter_id="E">110</value>\n+<value letter_id="F">77</value>\n+<value letter_id="G">-521</value>\n+<value letter_id="H">-4</value>\n+<value letter_id="I">147</value>\n+<value letter_id="K">95</value>\n+<value letter_id="L">201</value>\n+<value letter_id="M">90</value>\n+<value letter_id="N">121</value>\n+<value le'..b'etter_ref letter_id="A"/>\n+</site>\n+<right_flank>GC</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_5" position="0" strand="none" pvalue="3.82e-05" >\n+<left_flank></left_flank>\n+<site>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>ATGGTCCTGT</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_29" position="30" strand="none" pvalue="4.02e-05" >\n+<left_flank>GCTGCCGGTG</left_flank>\n+<site>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+</site>\n+<right_flank>GCCCTGGCG</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_1" position="27" strand="none" pvalue="5.52e-05" >\n+<left_flank>AGTCACAAGT</left_flank>\n+<site>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>GGGTCGCACG</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_3" position="14" strand="none" pvalue="5.94e-05" >\n+<left_flank>CCCAGGTTTC</left_flank>\n+<site>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>TCGCCGCACC</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_16" position="22" strand="none" pvalue="6.78e-05" >\n+<left_flank>AGTTTCAGTT</left_flank>\n+<site>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>attatataac</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_7" position="2" strand="none" pvalue="2.08e-04" >\n+<left_flank>TC</left_flank>\n+<site>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+</site>\n+<right_flank>AAATGTTCCT</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_8" position="13" strand="none" pvalue="4.05e-04" >\n+<left_flank>TATAACTCAG</left_flank>\n+<site>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>TAATTTGTAC</right_flank>\n+</contributing_site>\n+</contributing_sites>\n+</motif>\n </motifs>\n <scanned_sites_summary p_thresh="0.0001">\n <scanned_sites sequence_id="sequence_0" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="39" pvalue="3.06e-05"/>\n' |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_test2.html --- a/test-data/meme_output_test2.html Thu Aug 29 10:19:55 2024 +0000 +++ b/test-data/meme_output_test2.html Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| b'@@ -1,3 +1,9508 @@\n+ * See http://stackoverflow.com/a/5450113/66387\n+ * Does string multiplication like the perl x operator.\n+ */\n+function string_mult(pattern, count) {\n+ if (count < 1) return \'\';\n+ var result = \'\';\n+ while (count > 1) {\n+ if (count & 1) result += pattern;\n+ count >>= 1, pattern += pattern;\n+ }\n+ return result + pattern;\n+}\n+\n+/*\n+ * See http://stackoverflow.com/questions/814613/how-to-read-get-data-from-a-url-using-javascript\n+ * Slightly modified with information from\n+ * https://developer.mozilla.org/en/DOM/window.location\n+ */\n+function parse_params() {\n+ "use strict";\n+ var search, queryStart, queryEnd, query, params, nvPairs, i, nv, n, v;\n+ search = window.location.search;\n+ queryStart = search.indexOf("?") + 1;\n+ queryEnd = search.indexOf("#") + 1 || search.length + 1;\n+ query = search.slice(queryStart, queryEnd - 1);\n+\n+ if (query === search || query === "") return {};\n+\n+ params = {};\n+ nvPairs = query.replace(/\\+/g, " ").split("&");\n+\n+ for (i = 0; i < nvPairs.length; i++) {\n+ nv = nvPairs[i].split("=");\n+ n = decodeURIComponent(nv[0]);\n+ v = decodeURIComponent(nv[1]);\n+ // allow a name to be used multiple times\n+ // storing each value in the array\n+ if (!(n in params)) {\n+ params[n] = [];\n+ }\n+ params[n].push(nv.length === 2 ? v : null);\n+ }\n+ return params;\n+}\n+\n+/*\n+ * coords\n+ *\n+ * Calculates the x and y offset of an element.\n+ * From http://www.quirksmode.org/js/findpos.html\n+ * with alterations to take into account scrolling regions\n+ */\n+function coords(elem) {\n+ var myX = myY = 0;\n+ if (elem.getBoundingClientRect) {\n+ var rect;\n+ rect = elem.getBoundingClientRect();\n+ myX = rect.left + ((typeof window.pageXOffset !== "undefined") ?\n+ window.pageXOffset : document.body.scrollLeft);\n+ myY = rect.top + ((typeof window.pageYOffset !== "undefined") ?\n+ window.pageYOffset : document.body.scrollTop);\n+ } else {\n+ // this fall back doesn\'t properly handle absolutely positioned elements\n+ // inside a scrollable box\n+ var node;\n+ if (elem.offsetParent) {\n+ // subtract all scrolling\n+ node = elem;\n+ do {\n+ myX -= node.scrollLeft ? node.scrollLeft : 0;\n+ myY -= node.scrollTop ? node.scrollTop : 0;\n+ } while (node = node.parentNode);\n+ // this will include the page scrolling (which is unwanted) so add it back on\n+ myX += (typeof window.pageXOffset !== "undefined") ? window.pageXOffset : document.body.scrollLeft;\n+ myY += (typeof window.pageYOffset !== "undefined") ? window.pageYOffset : document.body.scrollTop;\n+ // sum up offsets\n+ node = elem;\n+ do {\n+ myX += node.offsetLeft;\n+ myY += node.offsetTop;\n+ } while (node = node.offsetParent);\n+ }\n+ }\n+ return [myX, myY];\n+}\n+\n+/*\n+ * position_popup\n+ *\n+ * Positions a popup relative to an anchor element.\n+ *\n+ * The available positions are:\n+ * 0 - Centered below the anchor.\n+ */\n+function position_popup(anchor, popup, position) {\n+ "use strict";\n+ var a_x, a_y, a_w, a_h, p_x, p_y, p_w, p_h;\n+ var a_xy, spacer, margin, scrollbar, page_w;\n+ // define constants\n+ spacer = 5;\n+ margin = 15;\n+ scrollbar = 15;\n+ // define the positions and widths\n+ a_xy = coords(anchor);\n+ a_x = a_xy[0];\n+ a_y = a_xy[1];\n+ a_w = anchor.offsetWidth;\n+ a_h = anchor.offsetHeight;\n+ p_w = popup.offsetWidth;\n+ p_h = popup.offsetHeight;\n+ page_w = null;\n+ if (window.innerWidth) {\n+ page_w = window.innerWidth;\n+ } else if (document.body) {\n+ page_w = document.body.clientWidth;\n+ }\n+ // check the position type is defined\n+ if (typeof position !== "number") {\n+ position = 0;\n+ }\n+ // calculate the popup position\n+ switch (position) {\n+ case 1:\n+ p_x = a_x + a_w + spacer;\n+ p_y = a_y + (a_h / 2) - (p_h / 2);\n+ break;\n+ case 0:\n+ default:\n+ p_x = a_x + (a_w / 2) - (p_w / 2);\n+ p_y = a_y + a_h + spacer;\n+ break;\n'..b'Site Strand Handling</th>\n+ <td id="opt_strand">\n+ <span class="strand_none">This alphabet only has one strand</span>\n+ <span class="strand_given">Sites must be on the given strand</span>\n+ <span class="strand_both">Sites may be on either strand</span>\n+ </td>\n+ </tr>\n+ <tr>\n+ <th>Maximum Number of Motifs</th>\n+ <td id="opt_nmotifs"></td>\n+ </tr>\n+ <tr>\n+ <th>Motif E-value Threshold</th>\n+ <td id="opt_evt"></td>\n+ </tr>\n+ <tr>\n+ <th>Minimum Motif Width</th>\n+ <td id="opt_minw"></td>\n+ </tr>\n+ <tr>\n+ <th>Maximum Motif Width</th>\n+ <td id="opt_maxw"></td>\n+ </tr>\n+ <tr>\n+ <th>Minimum Sites per Motif</th>\n+ <td id="opt_minsites"></td>\n+ </tr>\n+ <tr>\n+ <th>Maximum Sites per Motif</th>\n+ <td id="opt_maxsites"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Bias on Number of Sites</th>\n+ <td id="opt_wnsites"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Sequence Prior</th>\n+ <td id="opt_prior">\n+ <span class="prior_dirichlet">Simple Dirichlet</span>\n+ <span class="prior_dmix">Dirichlet Mixture</span>\n+ <span class="prior_mega">Mega-weight Dirichlet Mixture</span>\n+ <span class="prior_megap">Mega-weight Dirichlet Mixture Plus</span>\n+ <span class="prior_addone">Add One</span>\n+ </td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Sequence Prior Source</th>\n+\t <td id="opt_prior_source"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Sequence Prior Strength</th>\n+ <td id="opt_b"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>EM Starting Point Source</th>\n+ <td id="opt_substring">\n+ <span class="substring_on">From substrings in input sequences</span>\n+ <span class="substring_off">From strings on command line (-cons)</span>\n+ </td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>EM Starting Point Map Type</th>\n+ <td id="opt_spmap">\n+ <span class="spmap_uni">Uniform</span>\n+ <span class="spmap_pam">Point Accepted Mutation</span>\n+ </td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>EM Starting Point Fuzz</th>\n+ <td id="opt_spfuzz"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>EM Maximum Iterations</th>\n+ <td id="opt_maxiter"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>EM Improvement Threshold</th>\n+ <td id="opt_distance"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Maximum Search Size</th>\n+ <td id="opt_searchsize"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Maximum Number of Sites for E-values</th>\n+ <td id="opt_csites"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Trim Gap Open Cost</th>\n+ <td id="opt_wg"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>Trim Gap Extend Cost</th>\n+ <td id="opt_ws"></td>\n+ </tr>\n+ <tr class="advanced">\n+ <th>End Gap Treatment</th>\n+ <td id="opt_noendgaps">\n+ <span class="noendgaps_on">No cost</span>\n+ <span class="noendgaps_off">Same cost as other gaps</span>\n+ </td>\n+ </tr>\n+ <tr>\n+ <td colspan="2" style="text-align: center">\n+ <a href="javascript:toggle_class(document.getElementById(\'tbl_settings\'), \'hide_advanced\')">\n+ <span class="show_more">Show Advanced Settings</span>\n+ <span class="show_less">Hide Advanced Settings</span>\n+ </a>\n+ </td>\n+ </tr>\n+ </table>\n <script>\n {\n $("opt_mod").className = data.options.mod;\n' |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_test2.txt --- a/test-data/meme_output_test2.txt Thu Aug 29 10:19:55 2024 +0000 +++ b/test-data/meme_output_test2.txt Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| b'@@ -1,40 +1,180 @@\n ********************************************************************************\n-SUMMARY OF MOTIFS\n+MOTIF GGSRTATAAAA MEME-1\twidth = 11 sites = 30 llr = 254 E-value = 5.1e-040\n ********************************************************************************\n+--------------------------------------------------------------------------------\n+\tMotif GGSRTATAAAA MEME-1 Description\n+--------------------------------------------------------------------------------\n+Simplified A 3313:9:a798\n+pos.-specific C 1:3::1:::1:\n+probability G 6756::::::2\n+matrix T 1:11a1a:3::\n+\n+ bits 2.2 * \n+ 2.0 * * \n+ 1.8 * * \n+ 1.5 * ** * \n+Relative 1.3 * ** * \n+Entropy 1.1 ****** \n+(12.2 bits) 0.9 * *******\n+ 0.7 * *******\n+ 0.4 ** ********\n+ 0.2 ***********\n+ 0.0 -----------\n+\n+Multilevel GGGGTATAAAA\n+consensus AACA T \n+sequence \n+ \n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGSRTATAAAA MEME-1 sites sorted by position p-value\n+--------------------------------------------------------------------------------\n+Sequence name Start P-value Site \n+------------- ----- --------- -----------\n+chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC\n+chr21_46031920_46031970_ 16 2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC\n+chr21_32202076_32202126_ 14 2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC\n+chr21_46057197_46057247_ 37 4.86e-06 ACAGGCCCTG GGCATATAAAA GCC \n+chr21_45993530_45993580_ 8 4.86e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA\n+chr21_45971413_45971463_ 10 4.86e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG\n+chr21_31964683_31964733_ 14 4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC\n+chr21_47517957_47518007_ 33 6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG \n+chr21_45978668_45978718_ 5 6.48e-06 CAGA GGGGTATAAAG GTTCCGACCA\n+chr21_32185595_32185645_ 19 6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT\n+chr21_32410820_32410870_ 22 1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA\n+chr21_31992870_31992920_ 17 1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC\n+chr21_19617074_19617124_ 40 1.41e-05 CCTCGGGACG TGGGTATATAA \n+chr21_31914206_31914256_ 16 1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG\n+chr21_46020421_46020471_ 3 1.95e-05 GA GACATATAAAA GCCAACATCC\n+chr21_32253899_32253949_ 18 1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA\n+chr21_45705687_45705737_ 38 2.16e-05 CGTGGTCGCG GGGGTATAACA GC \n+chr21_47575506_47575556_ 31 3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG \n+chr21_31744582_31744632_ 13 3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC\n+chr21_31768316_31768366_ 1 3.67e-05 . AACGTATATAA ATGGTCCTGT\n+chr21_26934381_26934431_ 28 3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG\n+chr21_31933633_31933683_ 5 5.65e-05 TCAG AGTATATATAA ATGTTCCTGT\n+chr21_31710037_31710087_ 15 6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC\n+chr21_36411748_36411798_ 23 7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac\n+chr21_46102103_46102153_ 37 1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT \n+chr21_46086869_46086919_ 38 1.39e-04 TGCCTGGGCC CAGGTATAAAG GC \n+chr21_37838750_37838800_ 3 4.81e-04 ga tggttttataa ggggcctcac\n+chr21_31962741_31962791_ 14 8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC\n+chr21_31973364_31973414_ 8 1.47e-03 aaactta aaactctataa acttaaaact\n+chr21_28217753_28217803_ 27 2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT\n+--------------------------------------------------------------------------------\n \n -----------------------------'..b'8 2_[+1]_37\n+chr21_31962741_31962791_ 0.00086 13_[+1]_26\n+chr21_31973364_31973414_ 0.0015 7_[+1]_32\n+chr21_28217753_28217803_ 0.0026 26_[+1]_13\n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGSRTATAAAA MEME-1 in BLOCKS format\n+--------------------------------------------------------------------------------\n+BL MOTIF GGSRTATAAAA width=11 seqs=30\n+chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 \n+chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 \n+chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 \n+chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 \n+chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 \n+chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 \n+chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 \n+chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 \n+chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 \n+chr21_32185595_32185645_ ( 19) GGGATATATAA 1 \n+chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 \n+chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 \n+chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 \n+chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 \n+chr21_46020421_46020471_ ( 3) GACATATAAAA 1 \n+chr21_32253899_32253949_ ( 18) AGGATATATAA 1 \n+chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 \n+chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 \n+chr21_31744582_31744632_ ( 13) AGCATATATAA 1 \n+chr21_31768316_31768366_ ( 1) AACGTATATAA 1 \n+chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 \n+chr21_31933633_31933683_ ( 5) AGTATATATAA 1 \n+chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 \n+chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 \n+chr21_46102103_46102153_ ( 37) CAGGTATAAAG 1 \n+chr21_46086869_46086919_ ( 38) CAGGTATAAAG 1 \n+chr21_37838750_37838800_ ( 3) TGGTTTTATAA 1 \n+chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 \n+chr21_31973364_31973414_ ( 8) AAACTCTATAA 1 \n+chr21_28217753_28217803_ ( 27) GGGGTTTCACT 1 \n+//\n+\n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGSRTATAAAA MEME-1 position-specific scoring matrix\n+--------------------------------------------------------------------------------\n+log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 \n+ -14 -179 114 -112 \n+ 3 -1155 137 -270 \n+ -114 20 86 -71 \n+ 3 -279 122 -170 \n+ -1155 -1155 -295 215 \n+ 156 -179 -1155 -170 \n+ -1155 -1155 -1155 220 \n+ 172 -279 -1155 -1155 \n+ 125 -1155 -1155 46 \n+ 167 -179 -1155 -1155 \n+ 144 -1155 -63 -270 \n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGSRTATAAAA MEME-1 position-specific probability matrix\n+--------------------------------------------------------------------------------\n+letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 \n+ 0.266667 0.066667 0.566667 0.100000 \n+ 0.300000 0.000000 0.666667 0.033333 \n+ 0.133333 0.266667 0.466667 0.133333 \n+ 0.300000 0.033333 0.600000 0.066667 \n+ 0.000000 0.000000 0.033333 0.966667 \n+ 0.866667 0.066667 0.000000 0.066667 \n+ 0.000000 0.000000 0.000000 1.000000 \n+ 0.966667 0.033333 0.000000 0.000000 \n+ 0.700000 0.000000 0.000000 0.300000 \n+ 0.933333 0.066667 0.000000 0.000000 \n+ 0.800000 0.000000 0.166667 0.033333 \n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif GGSRTATAAAA MEME-1 regular expression\n+--------------------------------------------------------------------------------\n+[GA][GA][GC][GA]TATA[AT]AA\n --------------------------------------------------------------------------------\n\\ No newline at end of file\n' |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/meme_output_test2.xml --- a/test-data/meme_output_test2.xml Thu Aug 29 10:19:55 2024 +0000 +++ b/test-data/meme_output_test2.xml Mon Jul 14 21:33:41 2025 +0000 |
| b |
| b'@@ -1,3 +1,658 @@\n+<alphabet_matrix>\n+<alphabet_array>\n+<value letter_id="A">-14</value>\n+<value letter_id="C">-179</value>\n+<value letter_id="G">114</value>\n+<value letter_id="T">-112</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">3</value>\n+<value letter_id="C">-1155</value>\n+<value letter_id="G">137</value>\n+<value letter_id="T">-270</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-114</value>\n+<value letter_id="C">20</value>\n+<value letter_id="G">86</value>\n+<value letter_id="T">-71</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">3</value>\n+<value letter_id="C">-279</value>\n+<value letter_id="G">122</value>\n+<value letter_id="T">-170</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-1155</value>\n+<value letter_id="C">-1155</value>\n+<value letter_id="G">-295</value>\n+<value letter_id="T">215</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">156</value>\n+<value letter_id="C">-179</value>\n+<value letter_id="G">-1155</value>\n+<value letter_id="T">-170</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">-1155</value>\n+<value letter_id="C">-1155</value>\n+<value letter_id="G">-1155</value>\n+<value letter_id="T">220</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">172</value>\n+<value letter_id="C">-279</value>\n+<value letter_id="G">-1155</value>\n+<value letter_id="T">-1155</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">125</value>\n+<value letter_id="C">-1155</value>\n+<value letter_id="G">-1155</value>\n+<value letter_id="T">46</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">167</value>\n+<value letter_id="C">-179</value>\n+<value letter_id="G">-1155</value>\n+<value letter_id="T">-1155</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">144</value>\n+<value letter_id="C">-1155</value>\n+<value letter_id="G">-63</value>\n+<value letter_id="T">-270</value>\n+</alphabet_array>\n+</alphabet_matrix>\n+</scores>\n+<probabilities>\n+<alphabet_matrix>\n+<alphabet_array>\n+<value letter_id="A">0.266667</value>\n+<value letter_id="C">0.066667</value>\n+<value letter_id="G">0.566667</value>\n+<value letter_id="T">0.100000</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.300000</value>\n+<value letter_id="C">0.000000</value>\n+<value letter_id="G">0.666667</value>\n+<value letter_id="T">0.033333</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.133333</value>\n+<value letter_id="C">0.266667</value>\n+<value letter_id="G">0.466667</value>\n+<value letter_id="T">0.133333</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.300000</value>\n+<value letter_id="C">0.033333</value>\n+<value letter_id="G">0.600000</value>\n+<value letter_id="T">0.066667</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.000000</value>\n+<value letter_id="C">0.000000</value>\n+<value letter_id="G">0.033333</value>\n+<value letter_id="T">0.966667</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.866667</value>\n+<value letter_id="C">0.066667</value>\n+<value letter_id="G">0.000000</value>\n+<value letter_id="T">0.066667</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.000000</value>\n+<value letter_id="C">0.000000</value>\n+<value letter_id="G">0.000000</value>\n+<value letter_id="T">1.000000</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.966667</value>\n+<value letter_id="C">0.033333</value>\n+<value letter_id="G">0.000000</value>\n+<value letter_id="T">0.000000</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.700000</value>\n+<value letter_id="C">0.000000</value>\n+<value letter_id="G">0.000000</value>\n+<value letter_id="T">0.300000</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value letter_id="A">0.933333</value>\n+<value letter_id="C">0.066667</value>\n+<value letter_id="G">0.000000</value>\n+<value letter_id="T">0.000000</value>\n+</alphabet_array>\n+<alphabet_array>\n+<value let'..b'r_ref letter_id="A"/>\n+</site>\n+<right_flank>TCGCCGCACC</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_16" position="22" strand="plus" pvalue="7.15e-05" >\n+<left_flank>AGTTTCAGTT</left_flank>\n+<site>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>attatataac</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_27" position="36" strand="plus" pvalue="1.39e-04" >\n+<left_flank>TGCCTGGGTC</left_flank>\n+<site>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+</site>\n+<right_flank>GCT</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_26" position="37" strand="plus" pvalue="1.39e-04" >\n+<left_flank>TGCCTGGGCC</left_flank>\n+<site>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="G"/>\n+</site>\n+<right_flank>GC</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_17" position="2" strand="plus" pvalue="4.81e-04" >\n+<left_flank>ga</left_flank>\n+<site>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>ggggcctcac</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_8" position="13" strand="plus" pvalue="8.57e-04" >\n+<left_flank>TATAACTCAG</left_flank>\n+<site>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>TAATTTGTAC</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_10" position="7" strand="plus" pvalue="1.47e-03" >\n+<left_flank>aaactta</left_flank>\n+<site>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="A"/>\n+</site>\n+<right_flank>acttaaaact</right_flank>\n+</contributing_site>\n+<contributing_site sequence_id="sequence_2" position="26" strand="plus" pvalue="2.64e-03" >\n+<left_flank>GGTGGGGGTG</left_flank>\n+<site>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="G"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="T"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="A"/>\n+<letter_ref letter_id="C"/>\n+<letter_ref letter_id="T"/>\n+</site>\n+<right_flank>GGTCCACTAT</right_flank>\n+</contributing_site>\n+</contributing_sites>\n+</motif>\n </motifs>\n <scanned_sites_summary p_thresh="0.0001">\n <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/>\n' |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_input_neg2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_input_neg2.fasta Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,66 @@ +>chr21_19617074_19617124_+ +AAAAATTATTACTAGGGAGGGGGCCGGAAAAACCTCGGGACGTGGGTATATAA +>chr21_26934381_26934431_+ +GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTTTCCmATAAAAGGGTCGCACGTT +>chr21_28217753_28217803_- +CAAAGGGGAGGAGTGmGGGTGGGGGTGGGGGTTTCACTGGTCCACTATAAA +>chr21_31710037_31710087_- +AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT +>chr21_31744582_31744632_- +CCCAGGTCTAAGAGCATATATAmACTTGGAGTCCAGACTATGACATTCAAA +>chr21_31768316_31768366_+ +AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAmAACTCAGAATCTT +>chr21_31914206_31914256_- +TGACACCCACTACTTAGAGTATAAAmATCATTCTGAGAAGTTAGAGACACC +>chr21_31933633_31933683_- +TCAGAGTATATATAAATGTTCCTGTCCAGTCACAAAGTCACCAAACTGACCT +>chr21_31962741_31962791_- +ACATATAACTCAGGTTGGATAAAATAATTTGTATCAGmCAAATCAGGAGAGTCAA +>chr21_31964683_31964733_+ +TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAmAGTGTCCATAC +>chr21_31973364_31973414_+ +aaacttaaaactctataaacttaaaactCTAGAATCCTGCTATAC +>chr21_31992870_31992920_+ +CTCATACACTATTGAAGATGTATAAAATTTCATTTGmGATGGTGACATT +>chr21_32185595_32185645_- +TCACCACCCACCAmAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA +>chr21_32202076_32202126_- +TGCCCACCAGCTATmGTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT +>chr21_32253899_32253949_- +AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC +>chr21_32410820_32410870_- +TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG +>chr21_36411748_36411798_- +ATAGTTCTGTATAAmGAGTTTCAGTTGGCATCtaaaaattatataactttattt +>chr21_37838750_37838800_- +gatggttttataaggggcctcaccctcggctcagccctcattcttctcct +>chr21_45705687_45705737_+ +CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGGGTATAACAGC +>chr21_45971413_45971463_- +CAGGCCCTGGGCATATAAAAGCCCCAGCAGmCCAACAGGctcacacacaca +>chr21_45978668_45978718_- +CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca +>chr21_45993530_45993580_+ +CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCTCGC +>chr21_46020421_46020471_+ +GAGACATATAAAAGCCAACATCCCTGAGCACCTAAACGGactcactc +>chr21_46031920_46031970_+ +GGAAAATACCCAGGGAGGGTATAAATCAGCAGCCAGGGCACACAAAC +>chr21_46046964_46047014_+ +ACAAGGCCAGGAGGGGTATAAAACTGAGAGCCCCAAGAACctcacaca +>chr21_46057197_46057247_+ +ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC +>chr21_46086869_46086919_- +GACGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC +>chr21_46102103_46102153_- +AGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGCGGGGTATAAAGGGGGCGG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCGTGAGCGTATAAAGGCCCTGGCG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGAGmGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_input_pos.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_input_pos.fasta Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,66 @@ +>chr21_19617074_19617124_+ +AAAAATTATTACTAGGGAGGGGGCCGGAACCTCGGGACGTGGGTATATAA +>chr21_26934381_26934431_+ +GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT +>chr21_28217753_28217803_- +CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTCCTATAAA +>chr21_31710037_31710087_- +AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT +>chr21_31744582_31744632_- +CCCAGGTCTAAGAGCATATATAACTTGGAGTCCAGACTATGACATTCAAA +>chr21_31768316_31768366_+ +AACGTATATAAATGGTCCTGTCCAGATGTG +>chr21_31914206_31914256_- +TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGACACC +>chr21_31933633_31933683_- +TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAATGACCT +>chr21_31962741_31962791_- +ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGGAGAGTCAA +>chr21_31964683_31964733_+ +TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTTAC +>chr21_31973364_31973414_+ +aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC +>chr21_31992870_31992920_+ +CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT +>chr21_32185595_32185645_- +TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTAGGAA +>chr21_32202076_32202126_- +TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT +>chr21_32253899_32253949_- +AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC +>chr21_32410820_32410870_- +TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG +>chr21_36411748_36411798_- +ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt +>chr21_37838750_37838800_- +gatggttttataaggggcctcaccctcggctcagccctcattcttctcct +>chr21_45705687_45705737_+ +CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGGGGTATAACAGC +>chr21_45971413_45971463_- +CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca +>chr21_45978668_45978718_- +CAGAGGGGTATAAAGGTTCCGACCACTCCTGGCACGAtcactca +>chr21_45993530_45993580_+ +CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCACTCGC +>chr21_46020421_46020471_+ +GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc +>chr21_46031920_46031970_+ +GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC +>chr21_46046964_46047014_+ +ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca +>chr21_46057197_46057247_+ +ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC +>chr21_46086869_46086919_- +GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC +>chr21_46102103_46102153_- +AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGTATAAAGGGGGCGG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_input_pos2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_input_pos2.fasta Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,66 @@ +>chr21_19617074_19617124_+ +AAAAATTATTACTAGGGAGGGGGCmGGAACCTCGGGACGTGGGTmATATAA +>chr21_26934381_26934431_+ +GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT +>chr21_28217753_28217803_- +CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTmCACTATAAA +>chr21_31710037_31710087_- +AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTTTT +>chr21_31744582_31744632_- +CCmAGGTCTAAGAGCATATATTAACTTGGAGTCCAGACTATGACATTCAAA +>chr21_31768316_31768366_+ +AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAAACTmAGAATCTT +>chr21_31914206_31914256_- +TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGA +>chr21_31933633_31933683_- +TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAAACTGACCT +>chr21_31962741_31962791_- +ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGG +>chr21_31964683_31964733_+ +TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTGTCCATAC +>chr21_31973364_31973414_+ +aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC +>chr21_31992870_31992920_+ +CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT +>chr21_32185595_32185645_- +TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA +>chr21_32202076_32202126_- +TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT +>chr21_32253899_32253949_- +AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC +>chr21_32410820_32410870_- +TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG +>chr21_36411748_36411798_- +ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt +>chr21_37838750_37838800_- +gatggttttataaggggcctcaccctcggctcagccctcattcttctcct +>chr21_45705687_45705737_+ +CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGmGGTATAACAGC +>chr21_45971413_45971463_- +CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca +>chr21_45978668_45978718_- +CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca +>chr21_45993530_45993580_+ +CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCmTCACTCACTCGC +>chr21_46020421_46020471_+ +GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc +>chr21_46031920_46031970_+ +GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC +>chr21_46046964_46047014_+ +ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca +>chr21_46057197_46057247_+ +ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCAT +>chr21_46086869_46086919_- +GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC +>chr21_46102103_46102153_- +AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTCCAGGTATAAAGGCT +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGmGG +>chr21_47517957_47518007_+ +CCTGGCGGCGmGGGCGGGTCAGGCCGGCGGGmGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGmGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGmGCGG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGmTGCCGGTGAGCmGTATAAAGGCCCTGGCG +>chr21_47575506_47575556_- +TGAGAAGCmGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGmGCCCTGGCG |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test1.html Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| @@ -0,0 +1,39 @@ + "train_negatives": { + "from": "shuffled", + "count": 33, + "positions": 1597 + }, + "test_positives": { + "count": 0, + "positions": 0 + }, + "test_negatives": { + "count": 0, + "positions": 0 + }, + "sequence_db": { + "freqs": [0.245, 0.255, 0.255, 0.245] + }, + "motifs": [ + { + "db": 0, + "id": "1-CTTTTATAYRCCY", + "alt": "STREME-1", + "width": 13, + "initial_width": 8, + "seed": "CTTTTATATGCCT", + "score_threshold": 10.1927, + "npassing": 18, + "train_pos_count": 18, + "train_neg_count": 0, + "train_log_pvalue": -6.81978, + "train_pvalue": "1.5e-007", + "train_dtc": -1.0, + "train_bernoulli": -1, + "test_pos_count": 0, + "test_neg_count": 0, + "test_log_pvalue": 0, + "test_pvalue": "1.0e+000", + "test_log_evalue": 0.69897, + "test_evalue": "5.0e+000", + "test_dtc": -1.0, \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test1.txt Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,93 @@ +******************************************************************************** +STREME - Sensitive, Thorough, Rapid, Enriched Motif Elicitation +******************************************************************************** +MEME version 5.5.8 (Release date: Thu May 15 15:01:46 2025 -0700) + +For further information on how to interpret these results please access https://meme-suite.org/meme. +To get a copy of the MEME Suite software please access https://meme-suite.org. + +******************************************************************************** + + +******************************************************************************** +REFERENCE +******************************************************************************** +If you use this program in your research, please cite: + +Timothy L. Bailey, +"STREME: accurate and versatile sequence motif discovery", +Bioinformatics, Mar. 24, 2021. +******************************************************************************** + + +ALPHABET= ACGT + +strands: + - + +Background letter frequencies +A 0.244 C 0.256 G 0.256 T 0.244 + +MOTIF 1-CTTTTATAYRCCY STREME-1 +letter-probability matrix: alength= 4 w= 13 nsites= 18 S= 1.5e-007 + 0.072963 0.851476 0.002598 0.072963 + 0.072963 0.145128 0.002598 0.779311 + 0.002486 0.002598 0.073075 0.921841 + 0.002486 0.002598 0.002598 0.992318 + 0.002486 0.002598 0.002598 0.992318 + 0.992318 0.002598 0.002598 0.002486 + 0.002486 0.002598 0.073075 0.921841 + 0.992318 0.002598 0.002598 0.002486 + 0.002486 0.497514 0.002598 0.497402 + 0.284394 0.143552 0.499090 0.072963 + 0.002486 0.710522 0.002598 0.284394 + 0.002486 0.779422 0.073075 0.145017 + 0.072963 0.428613 0.073075 0.425349 + +MOTIF 2-CCCCACCRSC STREME-2 +letter-probability matrix: alength= 4 w= 10 nsites= 12 S= 7.2e-005 + 0.139001 0.787776 0.070814 0.002409 + 0.070705 0.924368 0.002517 0.002409 + 0.002409 0.924368 0.070814 0.002409 + 0.002409 0.992664 0.002517 0.002409 + 0.716267 0.002517 0.210510 0.070705 + 0.002409 0.856072 0.070814 0.070705 + 0.208825 0.786248 0.002517 0.002409 + 0.343890 0.030359 0.555046 0.070705 + 0.070705 0.376471 0.550414 0.002409 + 0.208825 0.786248 0.002517 0.002409 + +MOTIF 3-RCAGAAKCA STREME-3 +letter-probability matrix: alength= 4 w= 9 nsites= 10 S= 4.4e-004 + 0.595835 0.003626 0.397069 0.003470 + 0.003470 0.694352 0.298708 0.003470 + 0.792557 0.003626 0.101987 0.101831 + 0.003470 0.101987 0.891074 0.003470 + 0.694196 0.003626 0.298708 0.003470 + 0.694196 0.298708 0.003626 0.003470 + 0.003470 0.101987 0.300909 0.593635 + 0.101831 0.792713 0.003626 0.101831 + 0.989279 0.003626 0.003626 0.003470 + +MOTIF 4-RAGTTATAAA STREME-4 +letter-probability matrix: alength= 4 w= 10 nsites= 8 S= 2.4e-003 + 0.333562 0.113112 0.440386 0.112939 + 0.988110 0.004021 0.004021 0.003848 + 0.003848 0.004021 0.879191 0.112939 + 0.003848 0.004021 0.222204 0.769927 + 0.112939 0.004021 0.004021 0.879018 + 0.769927 0.004021 0.113112 0.112939 + 0.003848 0.004021 0.113112 0.879018 + 0.988110 0.004021 0.004021 0.003848 + 0.549304 0.113112 0.113112 0.224471 + 0.769927 0.004021 0.113112 0.112939 + +MOTIF 5-AACCTCGG STREME-5 +letter-probability matrix: alength= 4 w= 8 nsites= 7 S= 5.5e-003 + 0.973700 0.008894 0.008894 0.008511 + 0.732403 0.250191 0.008894 0.008511 + 0.008511 0.974083 0.008894 0.008511 + 0.008511 0.974083 0.008894 0.008511 + 0.008511 0.008894 0.008894 0.973700 + 0.008511 0.732786 0.250191 0.008511 + 0.249809 0.008894 0.732786 0.008511 + 0.008511 0.008894 0.974083 0.008511 \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test1.xml Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,26 @@ + <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/> + <letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/> + <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/> + <letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/> + <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/> + <letter id="V" symbol="V" equals="ACG" name="Not T"/> + <letter id="H" symbol="H" equals="ACT" name="Not G"/> + <letter id="D" symbol="D" equals="AGT" name="Not C"/> + <letter id="B" symbol="B" equals="CGT" name="Not A"/> + <letter id="M" symbol="M" equals="AC" name="Amino"/> + <letter id="R" symbol="R" equals="AG" name="Purine"/> + <letter id="W" symbol="W" equals="AT" name="Weak"/> + <letter id="S" symbol="S" equals="CG" name="Strong"/> + <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/> + <letter id="K" symbol="K" equals="GT" name="Keto"/> + </alphabet> + <strands>both</strands> + <sequence_db A="0.245" C="0.255" G="0.255" T="0.245"/> + <background_frequencies source="--negatives--" order="2"> + <alphabet_array> + <value letter_id="A">0.244</value> + <value letter_id="C">0.256</value> + <value letter_id="G">0.256</value> + <value letter_id="T">0.244</value> + </alphabet_array> + </background_frequencies> \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test2.html Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| @@ -0,0 +1,43 @@ + "train_negatives": { + "from": "shuffled", + "count": 33, + "positions": 1597 + }, + "test_positives": { + "count": 0, + "positions": 0 + }, + "test_negatives": { + "count": 0, + "positions": 0 + }, + "sequence_db": { + "freqs": [ + 0.218, 0.24, 0.24, 0.218, 0.0266, 0.0125, 0, 0.00313, 0, 0, + 0.0266, 0, 0, 0, 0.0125, 0.00313 + ] + }, + "motifs": [ + { + "db": 0, + "id": "1-GTATAAAAGC", + "alt": "STREME-1", + "width": 10, + "initial_width": 5, + "seed": "GTATAAAGGC", + "score_threshold": 9.73039, + "npassing": 28, + "train_pos_count": 28, + "train_neg_count": 0, + "train_log_pvalue": -13.1578, + "train_pvalue": "7.0e-014", + "train_dtc": -1.0, + "train_bernoulli": -1, + "test_pos_count": 0, + "test_neg_count": 0, + "test_log_pvalue": 0, + "test_pvalue": "1.0e+000", + "test_log_evalue": 0.477121, + "test_evalue": "3.0e+000", + "test_dtc": -1.0, + "test_bernoulli": -1, \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test2.txt Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,78 @@ +******************************************************************************** +STREME - Sensitive, Thorough, Rapid, Enriched Motif Elicitation +******************************************************************************** +MEME version 5.5.8 (Release date: Thu May 15 15:01:46 2025 -0700) + +For further information on how to interpret these results please access https://meme-suite.org/meme. +To get a copy of the MEME Suite software please access https://meme-suite.org. + +******************************************************************************** + + +******************************************************************************** +REFERENCE +******************************************************************************** +If you use this program in your research, please cite: + +Timothy L. Bailey, +"STREME: accurate and versatile sequence motif discovery", +Bioinformatics, Mar. 24, 2021. +******************************************************************************** + + +******************************************************************************** +ALPHABET "DNA with covalent modifications" DNA-LIKE +******************************************************************************** +A "Adenine" 8510A8 ~ T "Thymine" A89610 +C "Cytosine" A50026 ~ G "Guanine" 313695 +a "N6-methyladenine" 8510A8 ~ t "Thymine_lowercase" 756BB1 +c "5-Carboxylcytosine" FEE090 ~ 4 "Guanine:5-Carboxylcytosine" E0F3F8 +f "5-Formylcytosine" FDAE61 ~ 3 "Guanine:5-Formylcytosine" ABD9E9 +g "modified_g" 00897B ~ 5 "cytosine_lowercase" 53698A +h "5-Hydroxymethylcytosine" F46D43 ~ 2 "Guanine:5-Hydroxymethylcytosine" 74ADD1 +m "5-Methylcytosine" D73027 ~ 1 "Guanine:5-Methylcytosine" 4575B4 +? = ACGTacfghmt12345 +******************************************************************************** + +strands: + - + +Background letter frequencies +A 0.218 C 0.24 G 0.24 T 0.218 a 0.0266 c 0.0125 f 1.96e-05 g 0.00315 h 1.96e-05 m 1.96e-05 t 0.0266 1 1.96e-05 2 1.96e-05 3 1.96e-05 4 0.0125 5 0.00315 + +MOTIF 1-GTATAAAAGC STREME-1 +letter-probability matrix: alength= 16 w= 10 nsites= 28 S= 7.0e-014 + 0.344606 0.001172 0.618858 0.034950 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.001065 0.001172 0.001172 0.996177 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.996177 0.001172 0.001172 0.001065 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.001065 0.001172 0.001172 0.996177 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.996177 0.001172 0.001172 0.001065 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.928407 0.001172 0.035057 0.034950 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.860638 0.136711 0.001172 0.001065 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.548672 0.001172 0.313139 0.136603 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.068834 0.068941 0.725207 0.136603 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + 0.068834 0.485705 0.308443 0.136603 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015 + +MOTIF 2-CCCACCAGA STREME-2 +letter-probability matrix: alength= 16 w= 9 nsites= 20 S= 2.2e-007 + 0.001482 0.947685 0.048775 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.143970 0.805197 0.048775 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.095771 0.711962 0.143064 0.048626 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.947536 0.001631 0.048775 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.095771 0.710908 0.191263 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.001482 0.900540 0.001631 0.095771 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.663614 0.095920 0.096974 0.142915 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.095771 0.332697 0.569474 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + 0.473982 0.239462 0.143064 0.142915 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021 + +MOTIF 3-4a4t4a4a4T STREME-3 +letter-probability matrix: alength= 16 w= 10 nsites= 7 S= 5.5e-003 + 0.004400 0.004842 0.004842 0.004400 0.140510 0.000253 0.000000 0.000064 0.000000 0.000000 0.000537 0.000000 0.000000 0.000000 0.840087 0.000064 + 0.004400 0.004842 0.004842 0.004400 0.700399 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.000253 0.000064 + 0.004400 0.004842 0.004842 0.004400 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.000537 0.000000 0.000000 0.000000 0.980059 0.000064 + 0.004400 0.004842 0.004842 0.004400 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.840371 0.000000 0.000000 0.000000 0.140226 0.000064 + 0.004400 0.004842 0.004842 0.004400 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.700115 0.000064 + 0.004400 0.004842 0.004842 0.004400 0.560427 0.000253 0.000000 0.000064 0.000000 0.000000 0.420454 0.000000 0.000000 0.000000 0.000253 0.000064 + 0.004400 0.004842 0.004842 0.144372 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.560142 0.000064 + 0.004400 0.144814 0.144814 0.004400 0.420454 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.000253 0.000064 + 0.004400 0.144814 0.144814 0.144372 0.140510 0.000253 0.000000 0.000064 0.000000 0.000000 0.140510 0.000000 0.000000 0.000000 0.280198 0.000064 + 0.004400 0.144814 0.004842 0.284344 0.280482 0.000253 0.000000 0.000064 0.000000 0.000000 0.000537 0.000000 0.000000 0.000000 0.280198 0.000064 \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test2.xml Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,39 @@ + <alphabet name="DNA with covalent modifications" like="dna"> + <letter id="A" symbol="A" complement="T" name="Adenine" colour="8510A8"/> + <letter id="C" symbol="C" complement="G" name="Cytosine" colour="A50026"/> + <letter id="G" symbol="G" complement="C" name="Guanine" colour="313695"/> + <letter id="T" symbol="T" complement="A" name="Thymine" colour="A89610"/> + <letter id="a" symbol="a" complement="t" name="N6-methyladenine" colour="8510A8"/> + <letter id="c" symbol="c" complement="4" name="5-Carboxylcytosine" colour="FEE090"/> + <letter id="f" symbol="f" complement="3" name="5-Formylcytosine" colour="FDAE61"/> + <letter id="g" symbol="g" complement="5" name="modified_g" colour="00897B"/> + <letter id="h" symbol="h" complement="2" name="5-Hydroxymethylcytosine" colour="F46D43"/> + <letter id="m" symbol="m" complement="1" name="5-Methylcytosine" colour="D73027"/> + <letter id="t" symbol="t" complement="a" name="Thymine_lowercase" colour="756BB1"/> + <letter id="n1" symbol="1" complement="m" name="Guanine:5-Methylcytosine" colour="4575B4"/> + <letter id="n2" symbol="2" complement="h" name="Guanine:5-Hydroxymethylcytosine" colour="74ADD1"/> + <letter id="n3" symbol="3" complement="f" name="Guanine:5-Formylcytosine" colour="ABD9E9"/> + <letter id="n4" symbol="4" complement="c" name="Guanine:5-Carboxylcytosine" colour="E0F3F8"/> + <letter id="n5" symbol="5" complement="g" name="cytosine_lowercase" colour="53698A"/> + <letter id="x3F" symbol="?" equals="ACGTacfghmt12345"/> + </alphabet> + <strands>both</strands> + <sequence_db A="0.218" C="0.24" G="0.24" T="0.218" a="0.0266" c="0.0125" f="0" g="0.00313" h="0" m="0" t="0.0266" n1="0" n2="0" n3="0" n4="0.0125" n5="0.00313"/> + <background_frequencies source="--negatives--" order="0"> + <alphabet_array> + <value letter_id="A">0.218</value> + <value letter_id="C">0.24</value> + <value letter_id="G">0.24</value> + <value letter_id="T">0.218</value> + <value letter_id="a">0.0266</value> + <value letter_id="c">0.0125</value> + <value letter_id="f">1.96e-05</value> + <value letter_id="g">0.00315</value> + <value letter_id="h">1.96e-05</value> + <value letter_id="m">1.96e-05</value> + <value letter_id="t">0.0266</value> + <value letter_id="n1">1.96e-05</value> + <value letter_id="n2">1.96e-05</value> + <value letter_id="n3">1.96e-05</value> + <value letter_id="n4">0.0125</value> + <value letter_id="n5">0.00315</value> \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test3.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test3.html Mon Jul 14 21:33:41 2025 +0000 |
| [ |
| @@ -0,0 +1,38 @@ + "max_sites": 2, + "site_hist": [0, 6, 1], + "len": 5, + "nsites": 7, + "evalue": "0", + "pwm": [ + [ + 0.00775938, 0.00626088, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.979973, 8.41549e-07, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.000219631, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 8.41549e-07, 8.41549e-07, 0.00577435, 8.41549e-07, + 8.41549e-07, 8.41549e-07 + ], [ + 0.00775938, 0.588717, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.397517, 8.41549e-07, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.000219631, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 8.41549e-07, 8.41549e-07, 0.00577435, 8.41549e-07, + 8.41549e-07, 8.41549e-07 + ], [ + 0.00775938, 0.00626088, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.00777606, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 8.41549e-07, 0.972417, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 8.41549e-07, 8.41549e-07, 0.00577435, 8.41549e-07, + 8.41549e-07, 8.41549e-07 + ], [ + 0.00775938, 0.00626088, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.979973, 8.41549e-07, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.000219631, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 8.41549e-07, 8.41549e-07, 0.00577435, 8.41549e-07, + 8.41549e-07, 8.41549e-07 + ], [ + 0.00775938, 0.00626088, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.787258, 8.41549e-07, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 0.000219631, 8.41549e-07, 8.41549e-07, 8.41549e-07, + 8.41549e-07, 8.41549e-07, 0.19849, 8.41549e-07, 8.41549e-07, + 8.41549e-07 + ] + ] \ No newline at end of file |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test3.txt Mon Jul 14 21:33:41 2025 +0000 |
| b |
| b'@@ -0,0 +1,79 @@\n+********************************************************************************\n+STREME - Sensitive, Thorough, Rapid, Enriched Motif Elicitation\n+********************************************************************************\n+MEME version 5.5.8 (Release date: Thu May 15 15:01:46 2025 -0700)\n+\n+For further information on how to interpret these results please access https://meme-suite.org/meme.\n+To get a copy of the MEME Suite software please access https://meme-suite.org.\n+\n+********************************************************************************\n+\n+\n+********************************************************************************\n+REFERENCE\n+********************************************************************************\n+If you use this program in your research, please cite:\n+\n+Timothy L. Bailey,\n+"STREME: accurate and versatile sequence motif discovery",\n+Bioinformatics, Mar. 24, 2021.\n+********************************************************************************\n+\n+\n+ALPHABET= ACDEFGHIKLMNPQRSTVWY\n+\n+strands: +\n+\n+Background letter frequencies\n+A 0.279 C 0.225 D 3.03e-05 E 3.03e-05 F 3.03e-05 G 0.28 H 3.03e-05 I 3.03e-05 K 3.03e-05 L 3.03e-05 M 0.0079 N 3.03e-05 P 3.03e-05 Q 3.03e-05 R 3.03e-05 S 3.03e-05 T 0.208 V 3.03e-05 W 3.03e-05 Y 3.03e-05 \n+\n+MOTIF 1-GCMGG STREME-1\n+letter-probability matrix: alength= 20 w= 5 nsites= 7 S= 5.5e-003\n+ 0.007759 0.006261 0.000001 0.000001 0.000001 0.979973 0.000001 0.000001 0.000001 0.000001 0.000220 0.000001 0.000001 0.000001 0.000001 0.000001 0.005774 0.000001 0.000001 0.000001\n+ 0.007759 0.588717 0.000001 0.000001 0.000001 0.397517 0.000001 0.000001 0.000001 0.000001 0.000220 0.000001 0.000001 0.000001 0.000001 0.000001 0.005774 0.000001 0.000001 0.000001\n+ 0.007759 0.006261 0.000001 0.000001 0.000001 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0.000001 0.000001 0.006448 0.000001 0.000001 0.000001 0.000001 0.000182 0.000001 0.000001 0.000001 0.000001 0.000001 0.981733 0.000001 0.000001 0.000001\n+ 0.006434 0.277760 0.000001 0.000001 0.000001 0.166256 0.000001 0.000001 0.000001 0.000001 0.479605 0.000001 0.000001 0.000001 0.000001 0.000001 0.069935 0.000001 0.000001 0.000001\n+ 0.823572 0.164999 0.000001 0.000001 0.000001 0.006448 0.000001 0.000001 0.000001 0.000001 0.000182 0.000001 0.000001 0.000001 0.000001 0.000001 0.004788 0.000001 0.000001 0.000001\n+\n+MOTIF 3-GTATAAAATCA STREME-3\n+letter-probability matrix: alength= 20 w= 11 nsites= 8 S= 9.3e-002\n+ 0.008845 0.007137 0.000001 0.000001 0.000001 0.977170 0.000001 0.000001 0.000001 0.000001 0.000250 0.000001 0.000001 0.000001 0.000001 0.000001 0.006583 0.000001 0.000001 0.000001\n+ 0.008845 0.007137 0.000001 0.000001 0.000001 0.008864 0.000001 0.000001 0.000001 0.000001 0.000250 0.000001 0.000001 0.000001 0.000001 0.000001 0.974888 0.000001 0.000001 0.000001\n+ 0.977151 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0.000001 0.785344 0.000001 0.000001 0.000001 0.000001 0.000222 0.000001 0.000001 0.000001 0.000001 0.000001 0.005826 0.000001 0.000001 0.000001\n+ 0.007829 0.006317 0.000001 0.000001 0.000001 0.007846 0.000001 0.000001 0.000001 0.000001 0.000222 0.000001 0.000001 0.000001 0.000001 0.000001 0.977773 0.000001 0.000001 0.000001\n+ 0.087098 0.006317 0.000001 0.000001 0.000001 0.900525 0.000001 0.000001 0.000001 0.000001 0.000222 0.000001 0.000001 0.000001 0.000001 0.000001 0.005826 0.000001 0.000001 0.000001\n+\n+MOTIF 5-TCACACACA STREME-5\n+letter-probability matrix: alength= 20 w= 9 nsites= 5 S= 9.8e-002\n+ 0.007502 0.192368 0.000001 0.000001 0.000001 0.007518 0.000001 0.000001 0.000001 0.000001 0.000212 0.000001 0.000001 0.000001 0.000001 0.000001 0.792388 0.000001 0.000001 0.000001\n+ 0.193817 0.716905 0.000001 0.000001 0.000001 0.083471 0.000001 0.000001 0.000001 0.000001 0.000212 0.000001 0.000001 0.000001 0.000001 0.000001 0.005583 0.000001 0.000001 0.000001\n+ 0.794307 0.006053 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0.000001 0.000001 0.000001 0.000001 0.000001 0.005583 0.000001 0.000001 0.000001\n+ 0.532038 0.006053 0.000001 0.000001 0.000001 0.193833 0.000001 0.000001 0.000001 0.000001 0.000212 0.000001 0.000001 0.000001 0.000001 0.000001 0.267851 0.000001 0.000001 0.000001\n' |
| b |
| diff -r fd05b142b3a3 -r 0c97e5c18468 test-data/streme_output_test3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streme_output_test3.xml Mon Jul 14 21:33:41 2025 +0000 |
| b |
| @@ -0,0 +1,73 @@ + <letter id="A" symbol="A" name="Alanine" colour="0000CC"/> + <letter id="C" symbol="C" name="Cysteine" colour="0000CC"/> + <letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/> + <letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/> + <letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/> + <letter id="G" symbol="G" name="Glycine" colour="FFB300"/> + <letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/> + <letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/> + <letter id="K" symbol="K" name="Lysine" colour="CC0000"/> + <letter id="L" symbol="L" name="Leucine" colour="0000CC"/> + <letter id="M" symbol="M" name="Methionine" colour="0000CC"/> + <letter id="N" symbol="N" name="Asparagine" colour="008000"/> + <letter id="P" symbol="P" name="Proline" colour="FFFF00"/> + <letter id="Q" symbol="Q" name="Glutamine" colour="008000"/> + <letter id="R" symbol="R" name="Arginine" colour="CC0000"/> + <letter id="S" symbol="S" name="Serine" colour="008000"/> + <letter id="T" symbol="T" name="Threonine" colour="008000"/> + <letter id="V" symbol="V" name="Valine" colour="0000CC"/> + <letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/> + <letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/> + <letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/> + <letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/> + <letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/> + <letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/> + </alphabet> + <strands>none</strands> + <sequence_db A="0.275" C="0.224" D="0" E="0" F="0" G="0.283" H="0" I="0" K="0" L="0" M="0.00977" N="0" P="0" Q="0" R="0" S="0" T="0.209" V="0" W="0" Y="0"/> + <background_frequencies source="--negatives--" order="0"> + <alphabet_array> + <value letter_id="A">0.279</value> + <value letter_id="C">0.225</value> + <value letter_id="D">3.03e-05</value> + <value letter_id="E">3.03e-05</value> + <value letter_id="F">3.03e-05</value> + <value letter_id="G">0.28</value> + <value letter_id="H">3.03e-05</value> + <value letter_id="I">3.03e-05</value> + <value letter_id="K">3.03e-05</value> + <value letter_id="L">3.03e-05</value> + <value letter_id="M">0.0079</value> + <value letter_id="N">3.03e-05</value> + <value letter_id="P">3.03e-05</value> + <value letter_id="Q">3.03e-05</value> + <value letter_id="R">3.03e-05</value> + <value letter_id="S">3.03e-05</value> + <value letter_id="T">0.208</value> + <value letter_id="V">3.03e-05</value> + <value letter_id="W">3.03e-05</value> + <value letter_id="Y">3.03e-05</value> + </alphabet_array> + </background_frequencies> + <stop nmotifs="5"/> + <objfun>Differential Enrichment</objfun> + <test>Fisher Exact Test</test> + <minw>5</minw> + <maxw>20</maxw> + <kmer>1</kmer> + <hofract>0.1</hofract> + <neval>25</neval> + <nref>4</nref> + <niter>20</niter> + <patience>3</patience> + <seed>0</seed> + <notrim>no</notrim> + <useer>no</useer> + <minscore>0</minscore> + <ignore_depth>5</ignore_depth> + <nsubsets>1</nsubsets> + <min_pal_ratio>0.85</min_pal_ratio> + <max_pal_ed>5</max_pal_ed> + <cand>no</cand> + <experimental>no</experimental> + <totallength>0</totallength> \ No newline at end of file |