| Previous changeset 2:b48e673af4e8 (2018-05-17) Next changeset 4:e24560178fad (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0" |
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modified:
macros.xml test-data/dreme_output_test1.html test-data/dreme_output_test1.txt test-data/dreme_output_test1.xml test-data/dreme_output_test2.html test-data/dreme_output_test2.txt test-data/dreme_output_test2.xml test-data/fimo_output_test1.gff test-data/fimo_output_test1.html test-data/fimo_output_test1.txt test-data/fimo_output_test1.xml test-data/fimo_output_test2.gff test-data/fimo_output_test2.html test-data/fimo_output_test2.txt test-data/fimo_output_test2.xml test-data/fimo_output_test3.html test-data/fimo_output_test3.txt test-data/fimo_output_test3.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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| diff -r b48e673af4e8 -r ff2f53a32d0e macros.xml --- a/macros.xml Thu May 17 14:11:15 2018 -0400 +++ b/macros.xml Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,10 +1,9 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> - <token name="@WRAPPER_VERSION@">4.12.0</token> + <token name="@WRAPPER_VERSION@">5.0.5</token> <xml name="requirements"> <requirements> - <requirement type="package" version="1.3.23">graphicsmagick</requirement> - <requirement type="package" version="4.12.0">meme</requirement> + <requirement type="package" version="5.0.5">meme</requirement> <yield/> </requirements> </xml> |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/dreme_output_test1.html --- a/test-data/dreme_output_test1.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/dreme_output_test1.html Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -7,10 +7,9 @@\n // @JSON_VAR data\n var data = {\n "program": "dreme",\n- "version": "4.12.0",\n- "release": "Tue Jun 27 16:22:50 2017 -0700",\n+ "version": "5.0.5",\n "cmd": [\n- "dreme", "-o", "./dreme_test1_out", "-p", "dreme_test_sites.fa",\n+ "dreme", "-o", "./dreme_out", "-p",\n "-norc", "-rna", "-s", "1"\n ],\n "options": {\n@@ -20,95 +19,19 @@\n "seed": 1,\n "stop": {\n "evalue": "0.05"\n- }\n- },\n "alphabet": {\n "name": "RNA",\n "like": "rna",\n "ncore": 4,\n "symbols": [\n- {\n- "symbol": "A",\n- "name": "Adenine",\n- "colour": "CC0000"\n- }, {\n- "symbol": "C",\n- "name": "Cytosine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "G",\n- "name": "Guanine",\n- "colour": "FFB300"\n- }, {\n- "symbol": "U",\n- "aliases": "T",\n- "name": "Uracil",\n- "colour": "008000"\n- }, {\n- "symbol": "N",\n- "aliases": "X.",\n- "name": "Any base",\n- "equals": "ACGU"\n- }, {\n- "symbol": "V",\n- "name": "Not U",\n- "equals": "ACG"\n- }, {\n- "symbol": "H",\n- "name": "Not G",\n- "equals": "ACU"\n- }, {\n- "symbol": "D",\n- "name": "Not C",\n- "equals": "AGU"\n- }, {\n- "symbol": "B",\n- "name": "Not A",\n- "equals": "CGU"\n- }, {\n- "symbol": "M",\n- "name": "Amino",\n- "equals": "AC"\n- }, {\n- "symbol": "R",\n- "name": "Purine",\n- "equals": "AG"\n- }, {\n- "symbol": "W",\n- "name": "Weak",\n- "equals": "AU"\n- }, {\n- "symbol": "S",\n- "name": "Strong",\n- "equals": "CG"\n- }, {\n- "symbol": "Y",\n- "name": "Pyrimidine",\n- "equals": "CU"\n- }, {\n- "symbol": "K",\n- "name": "Keto",\n- "equals": "GU"\n- }\n- ]\n- },\n "background": {\n "freqs": [0.221, 0.245, 0.221, 0.312]\n- },\n- "sequence_db": {\n- "name": "dreme test sites",\n- "file": "dreme_test_sites.fa",\n- "lmod": "Thu Apr 26 15:09:03 CEST 2018",\n- "count": 1000\n- },\n "control_db": {\n "name": "shuffled positive sequences",\n "from": "shuffled",\n "count": 1000,\n "freqs": [0.221, 0.245, 0.221, 0.312]\n- },\n "motifs": [\n- {\n "db": 0,\n "id": "UUYUCY",\n "alt": "DREME-1",\n@@ -126,9 +49,7 @@\n [0.000000, 0.000000, 0.000000, 1.000000], \n [0.000000, 1.000000, 0.000000, 0.000000], \n [0.000000, 0.474946, 0.000000, 0.525054]\n- ],\n "matches": [\n- {\n "seq": "UUUUCC",\n "p": 147,\n "n": 75,\n@@ -140,6059 +61,53 @@\n "n": 94,\n "pvalue": "2.2e-005",\n "evalue": "1.0e+000"\n- }, {\n "seq": "UUCUCU",\n "p": 94,\n "n": 51,\n "pvalue": "1.3e-004",\n "evalue": "6.1e+000"\n- }, {\n "seq": "UUCUCC",\n "p": 75,\n "n": 42,\n "pvalue": "1.1e-003",\n "evalue": "5.0e+001"\n- }\n- ]\n- }, {\n- "db": 0,\n- "id": "YAGG",\n- "alt": "DREME-2",\n- '..b'alphabet"></td>\n- <td id="ins_seq_count"></td>\n- </tr>\n- </table>\n- <script>\n- {\n- var db = data.sequence_db;\n- $("ins_seq_source").innerHTML = db.file;\n- $("ins_seq_alphabet").innerHTML = dreme_alphabet.get_alphabet_name();\n- $("ins_seq_count").innerHTML = db.count;\n- }\n- </script>\n- <h4>Control Sequences</h4>\n- <table id="seq_info" class="inputs">\n- <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>\n- <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>\n- </tr>\n- <tr>\n- <td id="ins_cseq_source"></td>\n- <td id="ins_cseq_count"></td>\n- </tr>\n- </table>\n- <script>\n- {\n- var db = data.control_db;\n- if (db.from == "shuffled") {\n- $("ins_cseq_source").innerHTML = "Shuffled Sequences";\n- } else {\n- $("ins_cseq_source").innerHTML = db.file;\n- }\n- $("ins_cseq_count").innerHTML = db.count;\n- }\n- </script>\n- <h4>Background</h4>\n- <span id="alpha_bg"></span>\n- <script>\n- {\n- $("alpha_bg").appendChild(make_alpha_bg(dreme_alphabet, data.control_db.freqs));\n- }\n- </script>\n- <h4>Other Settings</h4>\n- <table id="tbl_settings" class="inputs hide_advanced">\n- <tr>\n- <th>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">Only the given strand is processed</span>\n- <span class="strand_both">Both the given and reverse complement strands are processed</span>\n- </td>\n- </tr>\n- <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>\n- <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>\n- <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>\n- <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>\n- <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>\n- </table>\n- <script>\n- {\n- $("opt_strand").className = (dreme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");\n- $("opt_ngen").innerHTML = data.options.ngen;\n- $("opt_seed").innerHTML = data.options.seed;\n- $("opt_stop_evalue").innerHTML = data.options.stop.evalue;\n- $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");\n- $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");\n- }\n- </script>\n- </div>\n- <!-- list information on this program -->\n- <div id="info_sec" class="bar" style="position:relative">\n- <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>\n- <div class="subsection">\n- <h5 id="version">DREME version</h5>\n- <span id="ins_version"></span> \n- (Release date: <span id="ins_release"></span>)<br>\n- </div>\n- <script>\n- $("ins_version").innerHTML = data["version"];\n- $("ins_release").innerHTML = data["release"];\n- </script>\n- <div class="subsection">\n- <h5 id="reference">Reference</h5>\n- <span class="citation">\n- Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.\n- <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a>\n- </span>\n- </div>\n- <div class="subsection">\n- <h5 id="command">Command line</h5>\n- <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">\n- </textarea>\n- <script>$("cmd").value = data["cmd"].join(" ");</script>\n- </div>\n- </div>\n- \n </body>\n </html>\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/dreme_output_test1.txt --- a/test-data/dreme_output_test1.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/dreme_output_test1.txt Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,12 +1,7 @@ -# DREME 4.12.0 -# command: dreme -o ./dreme_test1_out -p dreme_test_sites.fa -norc -rna -s 1 -# positives: 1000 from dreme_test_sites.fa (Thu Apr 26 15:09:03 CEST 2018) +# DREME 5.0.5 # negatives: 1000 from shuffled positives -# host: ThinkPad-T450s -# when: Thu May 03 13:22:29 CEST 2018 -MEME version 4.12.0 - +MEME version 5.0.5 ALPHABET "RNA" RNA-LIKE A "Adenine" CC0000 C "Cytosine" 0000CC @@ -27,20 +22,15 @@ K "Keto" = GU T = U END ALPHABET - Background letter frequencies (from dataset): A 0.221 C 0.245 G 0.221 U 0.312 - - MOTIF UUYUCY DREME-1 - # Word Pos Neg P-value E-value # BEST UUYUCY 387 210 2.6e-018 1.2e-013 # UUUUCC 147 75 1.8e-007 8.1e-003 # UUUUCU 155 94 2.2e-005 1.0e+000 # UUCUCU 94 51 1.3e-004 6.1e+000 # UUCUCC 75 42 1.1e-003 5.0e+001 - letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 @@ -48,29 +38,21 @@ 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.474946 0.000000 0.525054 - - MOTIF YAGG DREME-2 - # Word Pos Neg P-value E-value # BEST YAGG 600 416 1.1e-016 5.1e-012 # CAGG 441 304 1.5e-010 6.6e-006 # UAGG 232 165 1.1e-004 4.7e+000 - letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012 0.000000 0.692308 0.000000 0.307692 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 - - MOTIF GAAGAW DREME-3 - # Word Pos Neg P-value E-value # BEST GAAGAW 81 22 8.2e-010 3.4e-005 # GAAGAU 45 7 2.4e-008 9.9e-004 # GAAGAA 40 16 7.9e-004 3.3e+001 - letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 @@ -78,17 +60,13 @@ 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.494382 0.000000 0.000000 0.505618 - - MOTIF SMUGGA DREME-4 - # Word Pos Neg P-value E-value # BEST SMUGGA 110 47 9.1e-008 3.7e-003 # GAUGGA 22 6 1.7e-003 7.1e+001 # GCUGGA 33 14 3.6e-003 1.5e+002 # CCUGGA 32 15 8.6e-003 3.5e+002 # CAUGGA 29 13 9.1e-003 3.7e+002 - letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003 0.000000 0.529412 0.470588 0.000000 0.428571 0.571429 0.000000 0.000000 @@ -96,7 +74,4 @@ 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 - - # Stopping reason: E-value threshold exceeded -# Running time: 13.95 seconds |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/dreme_output_test1.xml --- a/test-data/dreme_output_test1.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/dreme_output_test1.xml Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,7 +1,5 @@ -<dreme version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> +<dreme version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> <model> - <command_line>dreme -o ./dreme_test1_out -p dreme_test_sites.fa -norc -rna -s 1</command_line> - <positives name="dreme test sites" count="1000" file="dreme_test_sites.fa" last_mod_date="Thu Apr 26 15:09:03 CEST 2018" /> <negatives name="shuffled positive sequences" count="1000" from="shuffled"/> <alphabet name="RNA" like="rna"> <letter id="A" symbol="A" name="Adenine" colour="CC0000"/> @@ -26,8 +24,6 @@ <ngen>100</ngen> <add_pv_thresh>0.01</add_pv_thresh> <seed>1</seed> - <host>ThinkPad-T450s</host> - <when>Thu May 03 13:22:29 CEST 2018</when> </model> <motifs> <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="1.2e-013" unerased_evalue="1.2e-013"> @@ -73,5 +69,4 @@ <match seq="CAUGGA" p="29" n="13" pvalue="9.1e-003" evalue="3.7e+002"/> </motif> </motifs> - <run_time cpu="13.95" real="13.95" stop="evalue"/> </dreme> |
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| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/dreme_output_test2.html --- a/test-data/dreme_output_test2.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/dreme_output_test2.html Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -7,10 +7,10 @@\n // @JSON_VAR data\n var data = {\n "program": "dreme",\n- "version": "4.12.0",\n- "release": "Tue Jun 27 16:22:50 2017 -0700",\n+ "version": "5.0.5",\n+ "release": "Mon Mar 18 20:12:19 2019 -0700",\n "cmd": [\n- "dreme", "-o", "./dreme_test2_out", "-p", "dreme_test_sites.fa",\n+ "dreme", "-o", "./dreme_out", "-p",\n "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink",\n "4", "-maxk", "10"\n ],\n@@ -36,80 +36,57 @@\n "symbol": "C",\n "name": "Cytosine",\n "colour": "0000CC"\n- }, {\n "symbol": "G",\n "name": "Guanine",\n "colour": "FFB300"\n- }, {\n "symbol": "U",\n "aliases": "T",\n "name": "Uracil",\n "colour": "008000"\n- }, {\n "symbol": "N",\n "aliases": "X.",\n "name": "Any base",\n "equals": "ACGU"\n- }, {\n "symbol": "V",\n "name": "Not U",\n "equals": "ACG"\n- }, {\n "symbol": "H",\n "name": "Not G",\n "equals": "ACU"\n- }, {\n "symbol": "D",\n "name": "Not C",\n "equals": "AGU"\n- }, {\n "symbol": "B",\n "name": "Not A",\n "equals": "CGU"\n- }, {\n "symbol": "M",\n "name": "Amino",\n "equals": "AC"\n- }, {\n "symbol": "R",\n "name": "Purine",\n "equals": "AG"\n- }, {\n "symbol": "W",\n "name": "Weak",\n "equals": "AU"\n- }, {\n "symbol": "S",\n "name": "Strong",\n "equals": "CG"\n- }, {\n "symbol": "Y",\n "name": "Pyrimidine",\n "equals": "CU"\n- }, {\n "symbol": "K",\n "name": "Keto",\n "equals": "GU"\n- }\n- ]\n- },\n "background": {\n "freqs": [0.221, 0.245, 0.221, 0.312]\n- },\n "sequence_db": {\n- "name": "dreme test sites",\n- "file": "dreme_test_sites.fa",\n- "lmod": "Thu Apr 26 15:09:03 CEST 2018",\n "count": 1000\n- },\n "control_db": {\n "name": "shuffled positive sequences",\n "from": "shuffled",\n "count": 1000,\n "freqs": [0.221, 0.245, 0.221, 0.312]\n- },\n "motifs": [\n- {\n "db": 0,\n "id": "UUYUCY",\n "alt": "DREME-1",\n@@ -127,5993 +104,64 @@\n [0.000000, 0.000000, 0.000000, 1.000000], \n [0.000000, 1.000000, 0.000000, 0.000000], \n [0.000000, 0.474946, 0.000000, 0.525054]\n- ],\n "matches": [\n- {\n "seq": "UUUUCC",\n "p": 147,\n "n": 75,\n "pvalue": "1.8e-007",\n "evalue": "2.2e-002"\n- }, {\n- "seq": "UUUUCU",\n- "p": 155,\n- "n": 94,\n- "pvalue": "2.2e-005",\n- "evalue": "2.8e+000"\n- }, {\n- "seq": "UUCUCU",\n- "p": 94,\n- "n": 51,\n- "pvalue": "1.3e-004",\n- "evalue": "1.7e+001"\n- }, {\n- "seq": "UUCUCC",\n- "p": 75,\n- "n": 42,\n- "pvalue": "1.1e-003",\n- "evalue": "1.4e+002"\n- }\n- ]\n- }, {\n- "db": 0,\n- "id": "YAGG",\n- "alt": "DREME-2",\n- "len": 4,\n- "nsites": 793,\n- "evalue": "1.4e-011",\n- "p": 600,\n- '..b'alphabet"></td>\n- <td id="ins_seq_count"></td>\n- </tr>\n- </table>\n- <script>\n- {\n- var db = data.sequence_db;\n- $("ins_seq_source").innerHTML = db.file;\n- $("ins_seq_alphabet").innerHTML = dreme_alphabet.get_alphabet_name();\n- $("ins_seq_count").innerHTML = db.count;\n- }\n- </script>\n- <h4>Control Sequences</h4>\n- <table id="seq_info" class="inputs">\n- <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>\n- <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>\n- </tr>\n- <tr>\n- <td id="ins_cseq_source"></td>\n- <td id="ins_cseq_count"></td>\n- </tr>\n- </table>\n- <script>\n- {\n- var db = data.control_db;\n- if (db.from == "shuffled") {\n- $("ins_cseq_source").innerHTML = "Shuffled Sequences";\n- } else {\n- $("ins_cseq_source").innerHTML = db.file;\n- }\n- $("ins_cseq_count").innerHTML = db.count;\n- }\n- </script>\n- <h4>Background</h4>\n- <span id="alpha_bg"></span>\n- <script>\n- {\n- $("alpha_bg").appendChild(make_alpha_bg(dreme_alphabet, data.control_db.freqs));\n- }\n- </script>\n- <h4>Other Settings</h4>\n- <table id="tbl_settings" class="inputs hide_advanced">\n- <tr>\n- <th>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">Only the given strand is processed</span>\n- <span class="strand_both">Both the given and reverse complement strands are processed</span>\n- </td>\n- </tr>\n- <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>\n- <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>\n- <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>\n- <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>\n- <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>\n- </table>\n- <script>\n- {\n- $("opt_strand").className = (dreme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");\n- $("opt_ngen").innerHTML = data.options.ngen;\n- $("opt_seed").innerHTML = data.options.seed;\n- $("opt_stop_evalue").innerHTML = data.options.stop.evalue;\n- $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");\n- $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");\n- }\n- </script>\n- </div>\n- <!-- list information on this program -->\n- <div id="info_sec" class="bar" style="position:relative">\n- <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>\n- <div class="subsection">\n- <h5 id="version">DREME version</h5>\n- <span id="ins_version"></span> \n- (Release date: <span id="ins_release"></span>)<br>\n- </div>\n- <script>\n- $("ins_version").innerHTML = data["version"];\n- $("ins_release").innerHTML = data["release"];\n- </script>\n- <div class="subsection">\n- <h5 id="reference">Reference</h5>\n- <span class="citation">\n- Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.\n- <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a>\n- </span>\n- </div>\n- <div class="subsection">\n- <h5 id="command">Command line</h5>\n- <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">\n- </textarea>\n- <script>$("cmd").value = data["cmd"].join(" ");</script>\n- </div>\n- </div>\n- \n </body>\n </html>\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/dreme_output_test2.txt --- a/test-data/dreme_output_test2.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/dreme_output_test2.txt Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,12 +1,7 @@ -# DREME 4.12.0 -# command: dreme -o ./dreme_test2_out -p dreme_test_sites.fa -norc -rna -s 1 -e 1e-05 -g 100 -mink 4 -maxk 10 -# positives: 1000 from dreme_test_sites.fa (Thu Apr 26 15:09:03 CEST 2018) +# DREME 5.0.5 # negatives: 1000 from shuffled positives -# host: ThinkPad-T450s -# when: Thu May 03 13:22:11 CEST 2018 -MEME version 4.12.0 - +MEME version 5.0.5 ALPHABET "RNA" RNA-LIKE A "Adenine" CC0000 C "Cytosine" 0000CC @@ -27,20 +22,15 @@ K "Keto" = GU T = U END ALPHABET - Background letter frequencies (from dataset): A 0.221 C 0.245 G 0.221 U 0.312 - - MOTIF UUYUCY DREME-1 - # Word Pos Neg P-value E-value # BEST UUYUCY 387 210 2.6e-018 3.3e-013 # UUUUCC 147 75 1.8e-007 2.2e-002 # UUUUCU 155 94 2.2e-005 2.8e+000 # UUCUCU 94 51 1.3e-004 1.7e+001 # UUCUCC 75 42 1.1e-003 1.4e+002 - letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 3.3e-013 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 @@ -48,21 +38,14 @@ 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.474946 0.000000 0.525054 - - MOTIF YAGG DREME-2 - # Word Pos Neg P-value E-value # BEST YAGG 600 416 1.1e-016 1.4e-011 # CAGG 441 304 1.5e-010 1.8e-005 # UAGG 232 165 1.1e-004 1.3e+001 - letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 1.4e-011 0.000000 0.692308 0.000000 0.307692 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 - - # Stopping reason: E-value threshold exceeded -# Running time: 15.97 seconds |
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| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/dreme_output_test2.xml --- a/test-data/dreme_output_test2.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/dreme_output_test2.xml Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,7 +1,5 @@ -<dreme version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> +<dreme version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> <model> - <command_line>dreme -o ./dreme_test2_out -p dreme_test_sites.fa -norc -rna -s 1 -e 1e-05 -g 100 -mink 4 -maxk 10</command_line> - <positives name="dreme test sites" count="1000" file="dreme_test_sites.fa" last_mod_date="Thu Apr 26 15:09:03 CEST 2018" /> <negatives name="shuffled positive sequences" count="1000" from="shuffled"/> <alphabet name="RNA" like="rna"> <letter id="A" symbol="A" name="Adenine" colour="CC0000"/> @@ -26,8 +24,6 @@ <ngen>100</ngen> <add_pv_thresh>0.01</add_pv_thresh> <seed>1</seed> - <host>ThinkPad-T450s</host> - <when>Thu May 03 13:22:11 CEST 2018</when> </model> <motifs> <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="3.3e-013" unerased_evalue="3.3e-013"> @@ -51,5 +47,4 @@ <match seq="UAGG" p="232" n="165" pvalue="1.1e-004" evalue="1.3e+001"/> </motif> </motifs> - <run_time cpu="15.97" real="15.97" stop="evalue"/> </dreme> |
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| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test1.gff --- a/test-data/fimo_output_test1.gff Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test1.gff Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,9 +1,9 @@ ##gff-version 3 -chrM fimo nucleotide_motif 2299 2306 46.6 - . Name=TACTAAYM_chrM-;Alias=MEME-1;ID=TACTAAYM-MEME-1-1-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 6529 6536 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-2-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 7741 7748 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-3-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 13656 13663 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-4-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 13740 13747 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-5-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 6529 6536 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-1-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 7741 7748 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-2-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 13656 13663 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-3-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 13740 13747 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-4-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; +chrM fimo nucleotide_motif 2299 2306 46.6 - . Name=TACTAAYM_chrM-;Alias=MEME-1;ID=TACTAAYM-MEME-1-5-chrM;pvalue=2.18e-05;qvalue= 0.142;sequence=TACTAACA; chrM fimo nucleotide_motif 861 868 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-6-chrM;pvalue=3.96e-05;qvalue= 0.185;sequence=TACTAACC; chrM fimo nucleotide_motif 9346 9353 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-7-chrM;pvalue=3.96e-05;qvalue= 0.185;sequence=TACTAACC; chrM fimo nucleotide_motif 3767 3774 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-8-chrM;pvalue=6.62e-05;qvalue= 0.216;sequence=TACTAATA; |
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| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test1.html --- a/test-data/fimo_output_test1.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test1.html Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -7,9 +7,8 @@\n <style type="text/css">\n td.left {text-align: left;}\n td.right {text-align: right; padding-right: 1cm;}\n-</style>\n </head>\n-<body bgcolor="#D5F0FF">\n+<body color="#000000">\n <a name="top_buttons"></a>\n <hr>\n <table summary="buttons" align="left" cellspacing="0">\n@@ -17,98 +16,36 @@\n <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>\n <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>\n <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>\n+<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>\n+<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>\n </tr>\n </table>\n-<br/>\n-<br/>\n-<hr/>\n <center><big><b>FIMO - Motif search tool</b></big></center>\n-<hr>\n-<p>\n-FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)\n-</p>\n-<p>\n-For further information on how to interpret these results\n-or to get a copy of the FIMO software please access\n-<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>\n+FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)\n+For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>\n+To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>\n <p>If you use FIMO in your research, please cite the following paper:<br>\n Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,\n "FIMO: Scanning for occurrences of a given motif",\n <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.\n-<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>\n-<hr>\n <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>\n-<hr>\n-<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">\n-<p>\n- DATABASE hsa_chrM.fa\n- <br />\n Database contains 1 sequences, 16569 residues\n-</p>\n-<p>\n- MOTIFS meme_fimo_input_1.xml (DNA)\n- <table>\n- <thead>\n- <tr>\n- <th style="border-bottom: 1px dashed;">MOTIF</th>\n- <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>\n- <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >\n BEST POSSIBLE MATCH\n- </th>\n- </tr>\n- </thead>\n- <tbody>\n- <tr>\n- <td style="text-align:right;">TACTAAYM</td>\n- <td style="text-align:right;padding-left: 1em;">8</td>\n- <td style="text-align:left;padding-left: 1em;">TACTAACA</td>\n- </tr>\n- </tbody>\n- </table>\n-</p>\n-<p>\n Random model letter frequencies (--nrdb--):\n-<br/>\n-\n A 0.275 C 0.225 G 0.225 T 0.275 </p>\n-</div>\n-<hr>\n <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>\n-<hr>\n-<ul>\n-<li>\n There were 11 motif occurences with a p-value less than 0.0001.\n-\n The full set of motif occurences can be seen in the\n-tab-delimited plain text output file\n-<a href="fimo.txt">fimo.txt</a>, \n-the GFF file \n-<a href="fimo.gff">fimo.gff</a> \n-which may be suitable for uploading to the \n-<a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>\n-(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),\n-or the XML file \n-<a href="fimo.xml">fimo.xml</a>.\n-</li>\n-<li>\n-The p-value of a motif occurrence is defined as the\n+TSV (tab-delimited values) output file\n+The <i>p</i>-value of a motif occurrence is defined as the\n probability of a random sequence of the same length as the motif\n matching that position of the sequence with as good or better a score.\n-</li>\n-<li>\n The score for the match of a position in a sequence to a motif\n is computed by summing the appropriate entries from each column of\n the position-dependent scoring matrix that represents the motif.\n-</li>\n-<li>\n The q-value of a motif o'..b'e:x-large;font-family:monospace;">TACTAACC</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">TACTAAYM</td>\n- <td style="text-align:left;">MEME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">3767</td>\n- <td style="text-align:left;">3774</td>\n- <td style="text-align:left;">6.62e-05</td>\n- <td style="text-align:left;">0.216</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">TACTAAYM</td>\n- <td style="text-align:left;">MEME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">5497</td>\n- <td style="text-align:left;">5504</td>\n- <td style="text-align:left;">6.62e-05</td>\n- <td style="text-align:left;">0.216</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">TACTAAYM</td>\n- <td style="text-align:left;">MEME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">10105</td>\n- <td style="text-align:left;">10112</td>\n- <td style="text-align:left;">6.62e-05</td>\n- <td style="text-align:left;">0.216</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">TACTAAYM</td>\n- <td style="text-align:left;">MEME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">10959</td>\n- <td style="text-align:left;">10966</td>\n- <td style="text-align:left;">8.79e-05</td>\n- <td style="text-align:left;">0.261</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACT</td>\n- </tr>\n-</tbody>\n </table>\n-\n <hr>\n <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>\n-<hr>\n-<p>\n-Command line:\n-</p>\n-<pre>\n-fimo -oc fimo_test1_out meme_fimo_input_1.xml hsa_chrM.fa\n-</pre>\n-<p>\n-Settings:\n-</p>\n-<pre>\n-<table>\n- <tr>\n- <td style="padding-right: 2em">output_directory = fimo_test1_out</td>\n- <td style="padding-left: 5em; padding-right: 2em">MEME file name = meme_fimo_input_1.xml</td>\n- <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>\n- </tr> <tr>\n- <td style="padding-right: 2em">background file name = --nrdb--</td>\n- <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>\n- <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>\n- </tr> <tr>\n- <td style="padding-right: 2em">allow clobber = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">text only = false</td>\n- <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">threshold type = p-value</td>\n- <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>\n- <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">alpha = 1</td>\n- <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>\n- <td style="padding-left: 5em; padding-right: 2em"></td>\n- </tr>\n-\n-</table>\n-</pre>\n-<p>\n This information can be useful in the event you wish to report a\n problem with the FIMO software.\n-</p>\n-<hr>\n-<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>\n </body>\n </html>\n' |
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| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test1.txt --- a/test-data/fimo_output_test1.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test1.txt Wed Dec 11 18:04:34 2019 -0500 |
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| @@ -1,9 +1,9 @@ -# motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -TACTAAYM MEME-1 chrM 2299 2306 - 12.9701 2.18e-05 0.142 TACTAACA +motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence TACTAAYM MEME-1 chrM 6529 6536 + 12.9701 2.18e-05 0.142 TACTAACA TACTAAYM MEME-1 chrM 7741 7748 + 12.9701 2.18e-05 0.142 TACTAACA TACTAAYM MEME-1 chrM 13656 13663 + 12.9701 2.18e-05 0.142 TACTAACA TACTAAYM MEME-1 chrM 13740 13747 + 12.9701 2.18e-05 0.142 TACTAACA +TACTAAYM MEME-1 chrM 2299 2306 - 12.9701 2.18e-05 0.142 TACTAACA TACTAAYM MEME-1 chrM 861 868 + 12.2836 3.96e-05 0.185 TACTAACC TACTAAYM MEME-1 chrM 9346 9353 + 12.2836 3.96e-05 0.185 TACTAACC TACTAAYM MEME-1 chrM 3767 3774 + 11.7164 6.62e-05 0.216 TACTAATA |
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| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test1.xml --- a/test-data/fimo_output_test1.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test1.xml Wed Dec 11 18:04:34 2019 -0500 |
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| @@ -1,16 +1,12 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> <!-- Begin document body --> -<fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> +<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" > -<command-line>fimo -oc fimo_test1_out meme_fimo_input_1.xml hsa_chrM.fa</command-line> <settings> -<setting name="output directory">fimo_test1_out</setting> -<setting name="MEME file name">meme_fimo_input_1.xml</setting> -<setting name="sequence file name">hsa_chrM.fa</setting> <setting name="background file name">--nrdb--</setting> -<setting name="allow clobber">true</setting> +<setting name="allow clobber">false</setting> <setting name="compute q-values">true</setting> <setting name="parse genomic coord.">false</setting> <setting name="text only">false</setting> |
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| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test2.gff --- a/test-data/fimo_output_test2.gff Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test2.gff Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,12 +1,12 @@ ##gff-version 3 -chrM fimo nucleotide_motif 440 446 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-1-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 2093 2099 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-2-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 2299 2305 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-3-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 5186 5192 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-4-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 6530 6536 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-5-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 7742 7748 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-6-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 13657 13663 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-7-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 13741 13747 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-8-chrM;pvalue=8.2e-05;qvalue= 0.327;sequence=ACTAACA; -chrM fimo nucleotide_motif 510 516 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-1-chrM;pvalue=4.15e-05;qvalue= 0.668;sequence=CCAGCAC; -chrM fimo nucleotide_motif 5137 5143 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-2-chrM;pvalue=4.15e-05;qvalue= 0.668;sequence=CCAGCAC; +chrM fimo nucleotide_motif 440 446 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-1-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 2093 2099 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-2-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 2299 2305 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-3-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 5186 5192 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-4-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 6530 6536 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-5-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 7742 7748 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-6-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 13657 13663 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-7-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 13741 13747 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-8-chrM;pvalue=8.2e-05;qvalue= 0.332;sequence=ACTAACA; +chrM fimo nucleotide_motif 510 516 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-1-chrM;pvalue=4.15e-05;qvalue= 0.683;sequence=CCAGCAC; +chrM fimo nucleotide_motif 5137 5143 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-2-chrM;pvalue=4.15e-05;qvalue= 0.683;sequence=CCAGCAC; chrM fimo nucleotide_motif 4241 4247 40.3 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-3-chrM;pvalue=9.37e-05;qvalue= 1;sequence=CCAGCAT; |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test2.html --- a/test-data/fimo_output_test2.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test2.html Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -9,7 +9,7 @@\n td.right {text-align: right; padding-right: 1cm;}\n </style>\n </head>\n-<body bgcolor="#D5F0FF">\n+<body color="#000000">\n <a name="top_buttons"></a>\n <hr>\n <table summary="buttons" align="left" cellspacing="0">\n@@ -17,123 +17,44 @@\n <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>\n <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>\n <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>\n+<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>\n+<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>\n </tr>\n </table>\n-<br/>\n-<br/>\n-<hr/>\n <center><big><b>FIMO - Motif search tool</b></big></center>\n-<hr>\n-<p>\n-FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)\n-</p>\n-<p>\n-For further information on how to interpret these results\n-or to get a copy of the FIMO software please access\n-<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>\n+FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)\n+For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>\n+To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>\n <p>If you use FIMO in your research, please cite the following paper:<br>\n Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,\n "FIMO: Scanning for occurrences of a given motif",\n <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.\n-<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>\n-<hr>\n <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>\n-<hr>\n-<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">\n-<p>\n- DATABASE hsa_chrM.fa\n- <br />\n Database contains 1 sequences, 16569 residues\n-</p>\n-<p>\n- MOTIFS dreme_fimo_input_1.xml (DNA)\n <table>\n <thead>\n- <tr>\n- <th style="border-bottom: 1px dashed;">MOTIF</th>\n- <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>\n- <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >\n- BEST POSSIBLE MATCH\n- </th>\n- </tr>\n </thead>\n <tbody>\n- <tr>\n- <td style="text-align:right;">ACTAAYH</td>\n- <td style="text-align:right;padding-left: 1em;">7</td>\n- <td style="text-align:left;padding-left: 1em;">ACTAACA</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">YTAACA</td>\n- <td style="text-align:right;padding-left: 1em;">6</td>\n- <td style="text-align:left;padding-left: 1em;">TTAACA</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">TCTGT</td>\n- <td style="text-align:right;padding-left: 1em;">5</td>\n- <td style="text-align:left;padding-left: 1em;">TCTGT</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">SCCAGG</td>\n- <td style="text-align:right;padding-left: 1em;">6</td>\n- <td style="text-align:left;padding-left: 1em;">CCCAGG</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">CCAGCAY</td>\n- <td style="text-align:right;padding-left: 1em;">7</td>\n- <td style="text-align:left;padding-left: 1em;">CCAGCAC</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">GMATGT</td>\n- <td style="text-align:right;padding-left: 1em;">6</td>\n- <td style="text-align:left;padding-left: 1em;">GAATGT</td>\n- </tr>\n </tbody>\n </table>\n-</p>\n-<p>\n-Random model letter frequencies (fimo_background_probs_hsa_chrM.txt):\n-<br/>\n-\n A 0.278 C 0.222 G 0.222 T 0.278 </p>\n-</div>\n-<hr>\n <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>\n-<hr>\n-<ul>\n-<li>\n There were 11 motif occurences with a p-value le'..b'AYH</td>\n- <td style="text-align:left;">DREME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">7742</td>\n- <td style="text-align:left;">7748</td>\n- <td style="text-align:left;">8.2e-05</td>\n- <td style="text-align:left;">0.327</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">ACTAAYH</td>\n- <td style="text-align:left;">DREME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">13657</td>\n- <td style="text-align:left;">13663</td>\n- <td style="text-align:left;">8.2e-05</td>\n- <td style="text-align:left;">0.327</td>\n+ <td style="text-align:left;">0.332</td>\n <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>\n </tr>\n- <tr>\n- <td style="text-align:left;">ACTAAYH</td>\n- <td style="text-align:left;">DREME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">13741</td>\n- <td style="text-align:left;">13747</td>\n- <td style="text-align:left;">8.2e-05</td>\n- <td style="text-align:left;">0.327</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">CCAGCAY</td>\n- <td style="text-align:left;">DREME-5</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">4241</td>\n- <td style="text-align:left;">4247</td>\n- <td style="text-align:left;">9.37e-05</td>\n- <td style="text-align:left;">1</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAT</td>\n- </tr>\n-</tbody>\n-</table>\n-\n <hr>\n <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>\n-<hr>\n-<p>\n Command line:\n-</p>\n-<pre>\n-fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa\n-</pre>\n-<p>\n Settings:\n-</p>\n-<pre>\n-<table>\n- <tr>\n- <td style="padding-right: 2em">output_directory = fimo_test2_out</td>\n- <td style="padding-left: 5em; padding-right: 2em">MEME file name = dreme_fimo_input_1.xml</td>\n- <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>\n- </tr> <tr>\n- <td style="padding-right: 2em">background file name = fimo_background_probs_hsa_chrM.txt</td>\n- <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>\n- <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>\n- </tr> <tr>\n- <td style="padding-right: 2em">allow clobber = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">text only = false</td>\n- <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">threshold type = p-value</td>\n- <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>\n- <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">alpha = 1</td>\n- <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>\n- <td style="padding-left: 5em; padding-right: 2em"></td>\n- </tr>\n-\n-</table>\n-</pre>\n-<p>\n This information can be useful in the event you wish to report a\n problem with the FIMO software.\n-</p>\n-<hr>\n-<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>\n </body>\n </html>\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test2.txt --- a/test-data/fimo_output_test2.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test2.txt Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,12 +1,12 @@ -# motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -CCAGCAY DREME-5 chrM 510 516 + 13.5843 4.15e-05 0.668 CCAGCAC -CCAGCAY DREME-5 chrM 5137 5143 + 13.5843 4.15e-05 0.668 CCAGCAC -ACTAAYH DREME-1 chrM 440 446 + 11.7385 8.2e-05 0.327 ACTAACA -ACTAAYH DREME-1 chrM 2093 2099 - 11.7385 8.2e-05 0.327 ACTAACA -ACTAAYH DREME-1 chrM 2299 2305 - 11.7385 8.2e-05 0.327 ACTAACA -ACTAAYH DREME-1 chrM 5186 5192 + 11.7385 8.2e-05 0.327 ACTAACA -ACTAAYH DREME-1 chrM 6530 6536 + 11.7385 8.2e-05 0.327 ACTAACA -ACTAAYH DREME-1 chrM 7742 7748 + 11.7385 8.2e-05 0.327 ACTAACA -ACTAAYH DREME-1 chrM 13657 13663 + 11.7385 8.2e-05 0.327 ACTAACA -ACTAAYH DREME-1 chrM 13741 13747 + 11.7385 8.2e-05 0.327 ACTAACA +motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence +CCAGCAY DREME-5 chrM 510 516 + 13.5843 4.15e-05 0.683 CCAGCAC +CCAGCAY DREME-5 chrM 5137 5143 + 13.5843 4.15e-05 0.683 CCAGCAC +ACTAAYH DREME-1 chrM 440 446 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 2093 2099 - 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 2299 2305 - 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 5186 5192 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 6530 6536 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 7742 7748 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 13657 13663 + 11.7286 8.2e-05 0.332 ACTAACA +ACTAAYH DREME-1 chrM 13741 13747 + 11.7286 8.2e-05 0.332 ACTAACA CCAGCAY DREME-5 chrM 4241 4247 + 13.1461 9.37e-05 1 CCAGCAT |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test2.xml --- a/test-data/fimo_output_test2.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test2.xml Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,16 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> <!-- Begin document body --> -<fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> +<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" > -<command-line>fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa</command-line> <settings> -<setting name="output directory">fimo_test2_out</setting> -<setting name="MEME file name">dreme_fimo_input_1.xml</setting> -<setting name="sequence file name">hsa_chrM.fa</setting> -<setting name="background file name">fimo_background_probs_hsa_chrM.txt</setting> -<setting name="allow clobber">true</setting> +<setting name="allow clobber">false</setting> <setting name="compute q-values">true</setting> <setting name="parse genomic coord.">false</setting> <setting name="text only">false</setting> @@ -45,7 +40,6 @@ <motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/> <motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/> <motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/> -<background source="fimo_background_probs_hsa_chrM.txt"> <value letter="A">0.278</value> <value letter="C">0.222</value> <value letter="G">0.222</value> |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test3.html --- a/test-data/fimo_output_test3.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test3.html Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -5,48 +5,23 @@\n <meta charset="UTF-8">\n <title>FIMO Results</title>\n <style type="text/css">\n-td.left {text-align: left;}\n-td.right {text-align: right; padding-right: 1cm;}\n-</style>\n </head>\n-<body bgcolor="#D5F0FF">\n-<a name="top_buttons"></a>\n-<hr>\n-<table summary="buttons" align="left" cellspacing="0">\n-<tr>\n+<body color="#000000">\n <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>\n <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>\n <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>\n-</tr>\n-</table>\n-<br/>\n-<br/>\n-<hr/>\n+<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>\n+<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>\n <center><big><b>FIMO - Motif search tool</b></big></center>\n-<hr>\n-<p>\n-FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)\n-</p>\n-<p>\n-For further information on how to interpret these results\n-or to get a copy of the FIMO software please access\n-<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>\n+FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)\n+For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>\n+To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>\n <p>If you use FIMO in your research, please cite the following paper:<br>\n Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,\n "FIMO: Scanning for occurrences of a given motif",\n <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.\n-<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>\n-<hr>\n <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>\n-<hr>\n-<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">\n-<p>\n- DATABASE hsa_chrM.fa\n- <br />\n Database contains 1 sequences, 16569 residues\n-</p>\n-<p>\n- MOTIFS dreme_fimo_input_1.xml (DNA)\n <table>\n <thead>\n <tr>\n@@ -63,74 +38,29 @@\n <td style="text-align:right;padding-left: 1em;">7</td>\n <td style="text-align:left;padding-left: 1em;">ACTAACA</td>\n </tr>\n- <tr>\n- <td style="text-align:right;">YTAACA</td>\n- <td style="text-align:right;padding-left: 1em;">6</td>\n- <td style="text-align:left;padding-left: 1em;">TTAACA</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">TCTGT</td>\n- <td style="text-align:right;padding-left: 1em;">5</td>\n- <td style="text-align:left;padding-left: 1em;">TCTGT</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">SCCAGG</td>\n- <td style="text-align:right;padding-left: 1em;">6</td>\n- <td style="text-align:left;padding-left: 1em;">CCCAGG</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">CCAGCAY</td>\n- <td style="text-align:right;padding-left: 1em;">7</td>\n- <td style="text-align:left;padding-left: 1em;">CCAGCAC</td>\n- </tr>\n- <tr>\n- <td style="text-align:right;">GMATGT</td>\n- <td style="text-align:right;padding-left: 1em;">6</td>\n- <td style="text-align:left;padding-left: 1em;">GAATGT</td>\n- </tr>\n </tbody>\n </table>\n </p>\n <p>\n Random model letter frequencies (--uniform--):\n-<br/>\n-\n A 0.250 C 0.250 G 0.250 T 0.250 </p>\n-</div>\n-<hr>\n <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>\n-<hr>\n-<ul>\n-<li>\n There were 517 motif occurences with a p-value less than 0.01.\n-\n The full set of motif occurences can be seen in the\n-tab-delimited plain text output file\n-<a href="fimo.txt">fimo.txt</a>, \n-the GFF file \n-<a href="fimo.gff">fimo.gff</a> \n+TSV (tab-delimited values) output file\n+the GFF3 file \n which may be suitable for uploa'..b't;">ACTAAYH</td>\n- <td style="text-align:left;">DREME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">-</td>\n- <td style="text-align:left;">15892</td>\n- <td style="text-align:left;">15898</td>\n- <td style="text-align:left;">0.00922</td>\n- <td style="text-align:left;">0.559</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTACAA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">ACTAAYH</td>\n- <td style="text-align:left;">DREME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">15995</td>\n- <td style="text-align:left;">16001</td>\n- <td style="text-align:left;">0.00922</td>\n- <td style="text-align:left;">0.559</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">GCTAAGA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">ACTAAYH</td>\n- <td style="text-align:left;">DREME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">16269</td>\n- <td style="text-align:left;">16275</td>\n- <td style="text-align:left;">0.00922</td>\n- <td style="text-align:left;">0.559</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAGGA</td>\n- </tr>\n- <tr>\n- <td style="text-align:left;">ACTAAYH</td>\n- <td style="text-align:left;">DREME-1</td>\n- <td style="text-align:left;">chrM</td>\n- <td style="text-align:center;">+</td>\n- <td style="text-align:left;">16553</td>\n- <td style="text-align:left;">16559</td>\n- <td style="text-align:left;">0.00922</td>\n- <td style="text-align:left;">0.559</td>\n- <td style="text-align:left;font-size:x-large;font-family:monospace;">AATAAGA</td>\n- </tr>\n-</tbody>\n-</table>\n-\n-<hr>\n-<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>\n-<hr>\n-<p>\n-Command line:\n-</p>\n-<pre>\n-fimo -o ./fimo_test4_out --thresh 0.01 --bgfile --uniform-- --max-stored-scores 100000 --motif ACTAAYH --motif-pseudo 0.1 dreme_fimo_input_1.xml hsa_chrM.fa\n-</pre>\n-<p>\n-Settings:\n-</p>\n-<pre>\n-<table>\n- <tr>\n- <td style="padding-right: 2em">output_directory = ./fimo_test4_out</td>\n- <td style="padding-left: 5em; padding-right: 2em">MEME file name = dreme_fimo_input_1.xml</td>\n- <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>\n- </tr> <tr>\n- <td style="padding-right: 2em">background file name = --uniform--</td>\n- <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>\n- <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>\n- </tr> <tr>\n- <td style="padding-right: 2em">allow clobber = false</td>\n- <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">text only = false</td>\n- <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>\n- <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">threshold type = p-value</td>\n- <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.01</td>\n- <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>\n- </tr>\n- <tr>\n- <td style="padding-right: 2em">alpha = 1</td>\n- <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>\n- <td style="padding-left: 5em; padding-right: 2em"></td>\n- </tr>\n-\n-</table>\n-</pre>\n-<p>\n This information can be useful in the event you wish to report a\n problem with the FIMO software.\n-</p>\n-<hr>\n-<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>\n </body>\n </html>\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test3.txt --- a/test-data/fimo_output_test3.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test3.txt Wed Dec 11 18:04:34 2019 -0500 |
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| b'@@ -1,4 +1,4 @@\n-# motif_id\tmotif_alt_id\tsequence_name\tstart\tstop\tstrand\tscore\tp-value\tq-value\tmatched_sequence\n+motif_id\tmotif_alt_id\tsequence_name\tstart\tstop\tstrand\tscore\tp-value\tq-value\tmatched_sequence\n ACTAAYH\tDREME-1\tchrM\t440\t446\t+\t12.1831\t6.1e-05\t0.239\tACTAACA\n ACTAAYH\tDREME-1\tchrM\t2093\t2099\t-\t12.1831\t6.1e-05\t0.239\tACTAACA\n ACTAAYH\tDREME-1\tchrM\t2299\t2305\t-\t12.1831\t6.1e-05\t0.239\tACTAACA\n@@ -20,499 +20,3 @@\n ACTAAYH\tDREME-1\tchrM\t862\t868\t+\t11.2394\t0.000244\t0.294\tACTAACC\n ACTAAYH\tDREME-1\tchrM\t1832\t1838\t+\t11.2394\t0.000244\t0.294\tACTAACC\n ACTAAYH\tDREME-1\tchrM\t8679\t8685\t+\t11.2394\t0.000244\t0.294\tACTAACC\n-ACTAAYH\tDREME-1\tchrM\t8770\t8776\t+\t11.2394\t0.000244\t0.294\tACTAACC\n-ACTAAYH\tDREME-1\tchrM\t9347\t9353\t+\t11.2394\t0.000244\t0.294\tACTAACC\n-ACTAAYH\tDREME-1\tchrM\t9359\t9365\t+\t11.2394\t0.000244\t0.294\tACTAACC\n-ACTAAYH\tDREME-1\tchrM\t10302\t10308\t+\t11.2394\t0.000244\t0.294\tACTAACC\n-ACTAAYH\tDREME-1\tchrM\t14765\t14771\t+\t11.2394\t0.000244\t0.294\tACTAACC\n-ACTAAYH\tDREME-1\tchrM\t4466\t4472\t+\t10.8592\t0.000305\t0.302\tACTAATT\n-ACTAAYH\tDREME-1\tchrM\t11248\t11254\t+\t10.8592\t0.000305\t0.302\tACTAATT\n-ACTAAYH\tDREME-1\tchrM\t475\t481\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t7930\t7936\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t8649\t8655\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t8670\t8676\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t10768\t10774\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t11053\t11059\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t11101\t11107\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t12720\t12726\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t13149\t13155\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t14216\t14222\t+\t10.6479\t0.000366\t0.302\tACTAATC\n-ACTAAYH\tDREME-1\tchrM\t678\t684\t-\t-1.07042\t0.000549\t0.366\tACTAAGA\n-ACTAAYH\tDREME-1\tchrM\t1435\t1441\t+\t-1.07042\t0.000549\t0.366\tACTAAGA\n-ACTAAYH\tDREME-1\tchrM\t1524\t1530\t+\t-1.07042\t0.000549\t0.366\tACTAAAA\n-ACTAAYH\tDREME-1\tchrM\t2035\t2041\t-\t-1.07042\t0.000549\t0.366\tACTAAGA\n-ACTAAYH\tDREME-1\tchrM\t8440\t8446\t+\t-1.07042\t0.000549\t0.366\tACTAAAA\n-ACTAAYH\tDREME-1\tchrM\t9995\t10001\t-\t-1.07042\t0.000549\t0.366\tACTAAAA\n-ACTAAYH\tDREME-1\tchrM\t10225\t10231\t-\t-1.07042\t0.000549\t0.366\tACTAAGA\n-ACTAAYH\tDREME-1\tchrM\t12725\t12731\t-\t-1.07042\t0.000549\t0.366\tACTAAGA\n-ACTAAYH\tDREME-1\tchrM\t14393\t14399\t+\t-1.07042\t0.000549\t0.366\tACTAAAA\n-ACTAAYH\tDREME-1\tchrM\t2294\t2300\t+\t-1.30986\t0.00061\t0.398\tACTAATG\n-ACTAAYH\tDREME-1\tchrM\t206\t212\t-\t-1.80282\t0.00165\t0.441\tATTAACA\n-ACTAAYH\tDREME-1\tchrM\t237\t243\t+\t-1.80282\t0.00165\t0.441\tAATAACA\n-ACTAAYH\tDREME-1\tchrM\t370\t376\t+\t-1.80282\t0.00165\t0.441\tCCTAACA\n-ACTAAYH\tDREME-1\tchrM\t1630\t1636\t+\t-1.80282\t0.00165\t0.441\tACTTACA\n-ACTAAYH\tDREME-1\tchrM\t1702\t1708\t+\t-1.80282\t0.00165\t0.441\tACTACCA\n-ACTAAYH\tDREME-1\tchrM\t2309\t2315\t+\t-1.80282\t0.00165\t0.441\tAGTAACA\n-ACTAAYH\tDREME-1\tchrM\t2363\t2369\t+\t-1.80282\t0.00165\t0.441\tACTGACA\n-ACTAAYH\tDREME-1\tchrM\t2370\t2376\t+\t-1.80282\t0.00165\t0.441\tATTAACA\n-ACTAAYH\tDREME-1\tchrM\t2395\t2401\t+\t-1.80282\t0.00165\t0.441\tACCAACA\n-ACTAAYH\tDREME-1\tchrM\t2761\t2767\t+\t-1.80282\t0.00165\t0.441\tCCTAACA\n-ACTAAYH\tDREME-1\tchrM\t2784\t2790\t+\t-1.80282\t0.00165\t0.441\tACTACCA\n-ACTAAYH\tDREME-1\tchrM\t3191\t3197\t-\t-1.80282\t0.00165\t0.441\tACTAAGT\n-ACTAAYH\tDREME-1\tchrM\t3756\t3762\t+\t-1.80282\t0.00165\t0.441\tACTATCA\n-ACTAAYH\tDREME-1\tchrM\t3873\t3879\t+\t-1.80282\t0.00165\t0.441\tACTAGCA\n-ACTAAYH\tDREME-1\tchrM\t3991\t3997\t+\t-1.80282\t0.00165\t0.441\tACAAACA\n-ACTAAYH\tDREME-1\tchrM\t4445\t4451\t-\t-1.80282\t0.00165\t0.441\tACCAACA\n-ACTAAYH\tDREME-1\tchrM\t4734\t4740\t+\t-1.80282\t0.00165\t0.441\tACTACCA\n-ACTAAYH\tDREME-1\tchrM\t5061\t5067\t+\t-1.80282\t0.00165\t0.441\tCCTAACA\n-ACTAAYH\tDREME-1\tchrM\t5177\t5183\t+\t-1.80282\t0.00165\t0.441\tGCTAACA\n-ACTAAYH\tDREME-1\tchrM\t5391\t5397\t+\t-1.80282\t0.00165\t0.441\tTCTAACA\n-ACTAAYH\tDREME-1\tchrM\t5680\t5686\t+\t-1.80282\t0.00165\t0.441\tACAAACA\n-ACTAAYH\tDREME-1\tchrM\t5686\t5692\t-\t-1.80282\t0.00165\t0.441\tACTAAGT\n-ACTAAYH\tDREME-1\tchrM\t6595\t6601\t+\t-1.80282\t0.00165\t0.441\tACCAACA\n-ACTAAYH\tDREME-1\tchrM\t7146\t7152\t+\t-1.80282\t0.00165\t0.441\tACTATCA\n-ACTAAYH\tDREME-1\tchrM\t7286\t7292\t+\t-1.80282\t0.00165\t'..b'.559\tACAAAAA\n-ACTAAYH\tDREME-1\tchrM\t7581\t7587\t-\t-15.0563\t0.00922\t0.559\tATTAAGA\n-ACTAAYH\tDREME-1\tchrM\t7692\t7698\t-\t-15.0563\t0.00922\t0.559\tACTAGGA\n-ACTAAYH\tDREME-1\tchrM\t7800\t7806\t-\t-15.0563\t0.00922\t0.559\tACTAGGA\n-ACTAAYH\tDREME-1\tchrM\t8230\t8236\t+\t-15.0563\t0.00922\t0.559\tCCTAAAA\n-ACTAAYH\tDREME-1\tchrM\t8323\t8329\t-\t-15.0563\t0.00922\t0.559\tACTTAAA\n-ACTAAYH\tDREME-1\tchrM\t8335\t8341\t+\t-15.0563\t0.00922\t0.559\tATTAAGA\n-ACTAAYH\tDREME-1\tchrM\t8494\t8500\t+\t-15.0563\t0.00922\t0.559\tAATAAAA\n-ACTAAYH\tDREME-1\tchrM\t8521\t8527\t+\t-15.0563\t0.00922\t0.559\tACCAAAA\n-ACTAAYH\tDREME-1\tchrM\t8531\t8537\t+\t-15.0563\t0.00922\t0.559\tACGAAAA\n-ACTAAYH\tDREME-1\tchrM\t8757\t8763\t-\t-15.0563\t0.00922\t0.559\tAATAAAA\n-ACTAAYH\tDREME-1\tchrM\t8881\t8887\t+\t-15.0563\t0.00922\t0.559\tTCTAAGA\n-ACTAAYH\tDREME-1\tchrM\t8887\t8893\t+\t-15.0563\t0.00922\t0.559\tATTAAAA\n-ACTAAYH\tDREME-1\tchrM\t9173\t9179\t-\t-15.0563\t0.00922\t0.559\tACTAGAA\n-ACTAAYH\tDREME-1\tchrM\t9236\t9242\t+\t-15.0563\t0.00922\t0.559\tAGTAAAA\n-ACTAAYH\tDREME-1\tchrM\t9706\t9712\t-\t-15.0563\t0.00922\t0.559\tAGTAAAA\n-ACTAAYH\tDREME-1\tchrM\t9796\t9802\t-\t-15.0563\t0.00922\t0.559\tACAAAAA\n-ACTAAYH\tDREME-1\tchrM\t9987\t9993\t-\t-15.0563\t0.00922\t0.559\tAGTAAGA\n-ACTAAYH\tDREME-1\tchrM\t10075\t10081\t-\t-15.0563\t0.00922\t0.559\tATTAAAA\n-ACTAAYH\tDREME-1\tchrM\t10243\t10249\t-\t-15.0563\t0.00922\t0.559\tAATAAGA\n-ACTAAYH\tDREME-1\tchrM\t10333\t10339\t-\t-15.0563\t0.00922\t0.559\tAATAAGA\n-ACTAAYH\tDREME-1\tchrM\t10376\t10382\t+\t-15.0563\t0.00922\t0.559\tACTACAA\n-ACTAAYH\tDREME-1\tchrM\t10379\t10385\t+\t-15.0563\t0.00922\t0.559\tACAAAAA\n-ACTAAYH\tDREME-1\tchrM\t10630\t10636\t-\t-15.0563\t0.00922\t0.559\tGCTAAGA\n-ACTAAYH\tDREME-1\tchrM\t10762\t10768\t+\t-15.0563\t0.00922\t0.559\tGCTAAAA\n-ACTAAYH\tDREME-1\tchrM\t11029\t11035\t+\t-15.0563\t0.00922\t0.559\tACGAAAA\n-ACTAAYH\tDREME-1\tchrM\t11367\t11373\t-\t-15.0563\t0.00922\t0.559\tACTATAA\n-ACTAAYH\tDREME-1\tchrM\t11602\t11608\t+\t-15.0563\t0.00922\t0.559\tCCTAAAA\n-ACTAAYH\tDREME-1\tchrM\t11646\t11652\t-\t-15.0563\t0.00922\t0.559\tACTACGA\n-ACTAAYH\tDREME-1\tchrM\t11751\t11757\t+\t-15.0563\t0.00922\t0.559\tACTCAAA\n-ACTAAYH\tDREME-1\tchrM\t11757\t11763\t+\t-15.0563\t0.00922\t0.559\tACTACGA\n-ACTAAYH\tDREME-1\tchrM\t12152\t12158\t+\t-15.0563\t0.00922\t0.559\tACCAAAA\n-ACTAAYH\tDREME-1\tchrM\t12295\t12301\t-\t-15.0563\t0.00922\t0.559\tCCTAAGA\n-ACTAAYH\tDREME-1\tchrM\t12311\t12317\t-\t-15.0563\t0.00922\t0.559\tACCAAAA\n-ACTAAYH\tDREME-1\tchrM\t12327\t12333\t+\t-15.0563\t0.00922\t0.559\tAATAAAA\n-ACTAAYH\tDREME-1\tchrM\t12352\t12358\t+\t-15.0563\t0.00922\t0.559\tACTATAA\n-ACTAAYH\tDREME-1\tchrM\t12416\t12422\t+\t-15.0563\t0.00922\t0.559\tACAAAAA\n-ACTAAYH\tDREME-1\tchrM\t12509\t12515\t+\t-15.0563\t0.00922\t0.559\tACCAAGA\n-ACTAAYH\tDREME-1\tchrM\t12662\t12668\t+\t-15.0563\t0.00922\t0.559\tACTCAGA\n-ACTAAYH\tDREME-1\tchrM\t13109\t13115\t-\t-15.0563\t0.00922\t0.559\tAGTAAGA\n-ACTAAYH\tDREME-1\tchrM\t13263\t13269\t+\t-15.0563\t0.00922\t0.559\tACTAGGA\n-ACTAAYH\tDREME-1\tchrM\t13422\t13428\t+\t-15.0563\t0.00922\t0.559\tACTCAAA\n-ACTAAYH\tDREME-1\tchrM\t13667\t13673\t+\t-15.0563\t0.00922\t0.559\tACGAAAA\n-ACTAAYH\tDREME-1\tchrM\t13791\t13797\t+\t-15.0563\t0.00922\t0.559\tCCTAAAA\n-ACTAAYH\tDREME-1\tchrM\t13866\t13872\t+\t-15.0563\t0.00922\t0.559\tACTTAAA\n-ACTAAYH\tDREME-1\tchrM\t13872\t13878\t+\t-15.0563\t0.00922\t0.559\tAATAAAA\n-ACTAAYH\tDREME-1\tchrM\t13894\t13900\t-\t-15.0563\t0.00922\t0.559\tAATAAAA\n-ACTAAYH\tDREME-1\tchrM\t14007\t14013\t+\t-15.0563\t0.00922\t0.559\tACTAGAA\n-ACTAAYH\tDREME-1\tchrM\t14023\t14029\t+\t-15.0563\t0.00922\t0.559\tCCTAAAA\n-ACTAAYH\tDREME-1\tchrM\t14405\t14411\t+\t-15.0563\t0.00922\t0.559\tACCAAGA\n-ACTAAYH\tDREME-1\tchrM\t14501\t14507\t+\t-15.0563\t0.00922\t0.559\tATTAAAA\n-ACTAAYH\tDREME-1\tchrM\t14687\t14693\t+\t-15.0563\t0.00922\t0.559\tACTACAA\n-ACTAAYH\tDREME-1\tchrM\t14732\t14738\t+\t-15.0563\t0.00922\t0.559\tACTACAA\n-ACTAAYH\tDREME-1\tchrM\t14776\t14782\t+\t-15.0563\t0.00922\t0.559\tAATAAAA\n-ACTAAYH\tDREME-1\tchrM\t15072\t15078\t+\t-15.0563\t0.00922\t0.559\tACTCAGA\n-ACTAAYH\tDREME-1\tchrM\t15607\t15613\t+\t-15.0563\t0.00922\t0.559\tACTAGGA\n-ACTAAYH\tDREME-1\tchrM\t15874\t15880\t+\t-15.0563\t0.00922\t0.559\tACTCAAA\n-ACTAAYH\tDREME-1\tchrM\t15892\t15898\t-\t-15.0563\t0.00922\t0.559\tACTACAA\n-ACTAAYH\tDREME-1\tchrM\t15995\t16001\t+\t-15.0563\t0.00922\t0.559\tGCTAAGA\n-ACTAAYH\tDREME-1\tchrM\t16269\t16275\t+\t-15.0563\t0.00922\t0.559\tACTAGGA\n-ACTAAYH\tDREME-1\tchrM\t16553\t16559\t+\t-15.0563\t0.00922\t0.559\tAATAAGA\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/fimo_output_test3.xml --- a/test-data/fimo_output_test3.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test3.xml Wed Dec 11 18:04:34 2019 -0500 |
| b |
| @@ -1,14 +1,10 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> <!-- Begin document body --> -<fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> +<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" > -<command-line>fimo -o ./fimo_test4_out --thresh 0.01 --bgfile --uniform-- --max-stored-scores 100000 --motif ACTAAYH --motif-pseudo 0.1 dreme_fimo_input_1.xml hsa_chrM.fa</command-line> <settings> -<setting name="output directory">./fimo_test4_out</setting> -<setting name="MEME file name">dreme_fimo_input_1.xml</setting> -<setting name="sequence file name">hsa_chrM.fa</setting> <setting name="background file name">--uniform--</setting> <setting name="allow clobber">false</setting> <setting name="compute q-values">true</setting> |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/meme_output_test1.html --- a/test-data/meme_output_test1.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test1.html Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -7,7999 +7,18 @@\n // @JSON_VAR data\n var data = {\n "program": "MEME",\n- "version": "4.12.0",\n- "release": "Tue Jun 27 16:22:50 2017 -0700",\n+ "version": "5.0.5",\n+ "release": "Mon Mar 18 20:12:19 2019 -0700",\n "stop_reason": "Stopped because requested number of motifs (1) found.",\n "cmd": [\n- "meme", "meme_input_1.fasta", "-o", "meme_test1_out", "-nostatus",\n- "-maxsize", "1000000"\n+ "meme",\n+ "-o",\n+ "-nostatus", "-maxsize", "1000000"\n ],\n "options": {\n- "mod": "zoops",\n- "revcomp": false,\n- "nmotifs": 1,\n- "minw": 8,\n- "maxw": 50,\n- "minsites": 2,\n- "maxsites": 30,\n- "wnsites": 0.8,\n- "spmap": "pam",\n- "spfuzz": 120,\n- "maxwords": -1,\n- "prior": "megap",\n- "b": 7500,\n- "maxiter": 50,\n- "distance": 1e-05,\n- "wg": 11,\n- "ws": 1,\n- "noendgaps": false,\n- "substring": true\n- },\n- "alphabet": {\n- "name": "Protein",\n- "like": "protein",\n- "ncore": 20,\n- "symbols": [\n- {\n- "symbol": "A",\n- "name": "Alanine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "C",\n- "name": "Cysteine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "D",\n- "name": "Aspartic acid",\n- "colour": "FF00FF"\n- }, {\n- "symbol": "E",\n- "name": "Glutamic acid",\n- "colour": "FF00FF"\n- }, {\n- "symbol": "F",\n- "name": "Phenylalanine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "G",\n- "name": "Glycine",\n- "colour": "FFB300"\n- }, {\n- "symbol": "H",\n- "name": "Histidine",\n- "colour": "FFCCCC"\n- }, {\n- "symbol": "I",\n- "name": "Isoleucine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "K",\n- "name": "Lysine",\n- "colour": "CC0000"\n- }, {\n- "symbol": "L",\n- "name": "Leucine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "M",\n- "name": "Methionine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "N",\n- "name": "Asparagine",\n- "colour": "008000"\n- }, {\n- "symbol": "P",\n- "name": "Proline",\n- "colour": "FFFF00"\n- }, {\n- "symbol": "Q",\n- "name": "Glutamine",\n- "colour": "008000"\n- }, {\n- "symbol": "R",\n- "name": "Arginine",\n- "colour": "CC0000"\n- }, {\n- "symbol": "S",\n- "name": "Serine",\n- "colour": "008000"\n- }, {\n- "symbol": "T",\n- "name": "Threonine",\n- "colour": "008000"\n- }, {\n- "symbol": "V",\n- "name": "Valine",\n- "colour": "0000CC"\n- }, {\n- "symbol": "W",\n- "name": "Tryptophan",\n- "colour": "0000CC"\n- }, {\n- "symbol": "Y",\n- "name": "Tyrosine",\n- "colour": "33E6CC"\n- }, {\n- "symbol": "X",\n- "aliases": "*.",\n- "name": "Any amino acid",\n- "equals": "ACDEFGHIKLMNPQRSTVWY"\n- }, {\n- "symbol": "B",\n- "name": "Asparagine or Aspartic acid",\n- "equals": "DN"\n- }, {\n- "symbol": "Z",\n- "name": "Glutamine or Glutamic acid",\n- "equal'..b' <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>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- $("opt_strand").className = (meme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");\n- $("opt_nmotifs").textContent = data.options.nmotifs;\n- $("opt_evt").textContent = (typeof data.options.evt === "number" ? data.options.evt : "no limit");\n- $("opt_minw").textContent = data.options.minw;\n- $("opt_maxw").textContent = data.options.maxw;\n- $("opt_minsites").textContent = data.options.minsites;\n- $("opt_maxsites").textContent = data.options.maxsites;\n- $("opt_wnsites").textContent = data.options.wnsites;\n- $("opt_spmap").className = data.options.spmap;\n- $("opt_spfuzz").textContent = data.options.spfuzz;\n- $("opt_prior").className = data.options.prior;\n- $("opt_b").textContent = data.options.b;\n- $("opt_maxiter").textContent = data.options.maxiter;\n- $("opt_distance").textContent = data.options.distance;\n- $("opt_wg").textContent = data.options.wg;\n- $("opt_ws").textContent = data.options.ws;\n- $("opt_noendgaps").className = (data.options.noendgaps ? "on" : "off");\n- $("opt_substring").className = (data.options.substring ? "on" : "off");\n- }\n- </script>\n- </div>\n- <!-- list information on this program -->\n- <div id="info_sec" class="bar">\n- <div class="subsection">\n- <h5 id="version">MEME version</h5>\n- <span id="ins_version"></span> \n- (Release date: <span id="ins_release"></span>)<br>\n- </div>\n- <script>\n- $("ins_version").innerHTML = data["version"];\n- $("ins_release").innerHTML = data["release"];\n- </script>\n- <div class="subsection">\n- <h5 id="reference">Reference</h5>\n- <span class="citation">\n- Timothy L. Bailey and Charles Elkan, \n- "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", \n- <em>Proceedings of the Second International Conference on Intelligent Systems \n- for Molecular Biology</em>, pp. 28-36, AAAI Press, Menlo Park, California, 1994. \n- </span>\n- </div>\n- <div class="subsection">\n- <h5 id="command">Command line</h5>\n- <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly">\n- </textarea>\n- <script>$("cmd").value = data["cmd"].join(" ");</script>\n- </div>\n- </div>\n- \n- </body>\n-</html>\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/meme_output_test1.txt --- a/test-data/meme_output_test1.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test1.txt Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -1,325 +1,61 @@\n ********************************************************************************\n MEME - Motif discovery tool\n-********************************************************************************\n-MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700)\n-\n-For further information on how to interpret these results or to get\n-a copy of the MEME software please access http://meme-suite.org .\n-\n-This file may be used as input to the MAST algorithm for searching\n-sequence databases for matches to groups of motifs. MAST is available\n-for interactive use and downloading at http://meme-suite.org .\n-********************************************************************************\n-\n-\n-********************************************************************************\n+MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)\n REFERENCE\n-********************************************************************************\n-If you use this program in your research, please cite:\n-\n-Timothy L. Bailey and Charles Elkan,\n-"Fitting a mixture model by expectation maximization to discover\n-motifs in biopolymers", Proceedings of the Second International\n-Conference on Intelligent Systems for Molecular Biology, pp. 28-36,\n-AAAI Press, Menlo Park, California, 1994.\n-********************************************************************************\n-\n-\n-********************************************************************************\n TRAINING SET\n-********************************************************************************\n-DATAFILE= meme_input_1.fasta\n+CONTROL SEQUENCES= --none--\n ALPHABET= ACDEFGHIKLMNPQRSTVWY\n Sequence name Weight Length Sequence name Weight Length \n ------------- ------ ------ ------------- ------ ------ \n chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 \n-chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 \n-chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 \n-chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 \n-chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 \n-chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 \n-chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 \n-chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 \n-chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 \n-chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 \n-chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 \n-chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 \n-chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 \n-chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 \n-chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 \n-********************************************************************************\n-\n-********************************************************************************\n COMMAND LINE SUMMARY\n-********************************************************************************\n-This information can also be useful in the event you wish to report a\n-problem with the MEME software.\n-\n-command: meme meme_input_1.fasta -o meme_test1_out -nostatus -maxsize 1000000 \n-\n model: mod= zoops nmotifs= 1 evt= inf\n-object function= E-value of product of p-values\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-width: wg= 11 ws= 1 endgaps= yes\n nsites: minsites= 2 maxsites= 30 wnsites= 0.8\n theta: spmap= pam spfuzz= '..b'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-\n-\n-\n-\n-Time 0.77 secs.\n-\n-********************************************************************************\n-\n-\n-********************************************************************************\n SUMMARY OF MOTIFS\n-********************************************************************************\n-\n---------------------------------------------------------------------------------\n \tCombined block diagrams: non-overlapping sites with p-value < 0.0001\n---------------------------------------------------------------------------------\n SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM\n ------------- ---------------- -------------\n chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)]\n-chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12\n-chr21_28217753_28217803_ 7.29e-01 50\n-chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25\n-chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27\n-chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39\n-chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24\n-chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35\n-chr21_31962741_31962791_ 1.61e-02 50\n-chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26\n-chr21_31973364_31973414_ 1.99e-01 50\n-chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23\n-chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21\n-chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26\n-chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20\n-chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18\n-chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17\n-chr21_37838750_37838800_ 8.23e-02 50\n-chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2\n-chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30\n-chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35\n-chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32\n-chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37\n-chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24\n-chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27\n-chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3\n-chr21_46086869_46086919_ 4.30e-02 50\n-chr21_46102103_46102153_ 4.30e-02 50\n-chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7\n-chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9\n---------------------------------------------------------------------------------\n-\n-********************************************************************************\n-\n-\n-********************************************************************************\n Stopped because requested number of motifs (1) found.\n-********************************************************************************\n-\n-CPU: ThinkPad-T450s\n-\n-********************************************************************************\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/meme_output_test1.xml --- a/test-data/meme_output_test1.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test1.xml Wed Dec 11 18:04:34 2019 -0500 |
| b |
| b'@@ -10,136 +10,29 @@\n <!ATTLIST MEME \n version CDATA #REQUIRED\n release CDATA #REQUIRED\n->\n <!-- Training-set elements -->\n <!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>\n-<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED>\n-<!ELEMENT alphabet (letter*)>\n-<!ATTLIST alphabet name CDATA #REQUIRED>\n-<!ELEMENT ambigs (letter*)>\n-<!ELEMENT letter EMPTY>\n-<!ATTLIST letter id ID #REQUIRED>\n-<!ATTLIST letter symbol CDATA #REQUIRED>\n-<!ATTLIST letter equals CDATA #IMPLIED>\n-<!ATTLIST letter aliases CDATA #IMPLIED>\n-<!ATTLIST letter complement CDATA #IMPLIED>\n-<!ATTLIST letter name CDATA #IMPLIED>\n-<!ATTLIST letter colour CDATA #IMPLIED>\n-<!ELEMENT sequence EMPTY>\n-<!ATTLIST sequence id ID #REQUIRED\n name CDATA #REQUIRED\n length CDATA #REQUIRED\n weight CDATA #REQUIRED\n->\n <!ELEMENT letter_frequencies (alphabet_array)>\n-\n <!-- Model elements -->\n <!ELEMENT model (\n command_line,\n host,\n type,\n nmotifs,\n- evalue_threshold,\n- object_function,\n- spfun,\n- min_width,\n- max_width,\n- wg,\n- ws,\n- endgaps,\n- minsites,\n- maxsites,\n- wnsites,\n- spmap,\n- spfuzz,\n- prior,\n- beta,\n- maxiter,\n- distance,\n- num_sequences,\n- num_positions,\n- seed,\n- hsfrac,\n- maxwords,\n- maxsize,\n- csites,\n- strands,\n- priors_file,\n- reason_for_stopping,\n- back_order,\n- background_frequencies\n )>\n <!ELEMENT command_line (#PCDATA)*>\n <!ELEMENT host (#PCDATA)*>\n <!ELEMENT type (#PCDATA)*>\n <!ELEMENT nmotifs (#PCDATA)*>\n-<!ELEMENT evalue_threshold (#PCDATA)*>\n-<!ELEMENT object_function (#PCDATA)*>\n-<!ELEMENT spfun (#PCDATA)*>\n-<!ELEMENT min_width (#PCDATA)*>\n-<!ELEMENT max_width (#PCDATA)*>\n-<!ELEMENT wg (#PCDATA)*>\n-<!ELEMENT ws (#PCDATA)*>\n-<!ELEMENT endgaps (#PCDATA)*>\n-<!ELEMENT minsites (#PCDATA)*>\n-<!ELEMENT maxsites (#PCDATA)*>\n-<!ELEMENT wnsites (#PCDATA)*>\n-<!ELEMENT spmap (#PCDATA)*>\n-<!ELEMENT spfuzz (#PCDATA)*>\n-<!ELEMENT prior (#PCDATA)*>\n-<!ELEMENT beta (#PCDATA)*>\n-<!ELEMENT maxiter (#PCDATA)*>\n-<!ELEMENT distance (#PCDATA)*>\n-<!ELEMENT num_sequences (#PCDATA)*>\n-<!ELEMENT num_positions (#PCDATA)*>\n-<!ELEMENT seed (#PCDATA)*>\n-<!ELEMENT hsfrac (#PCDATA)*>\n-<!ELEMENT maxwords (#PCDATA)*>\n-<!ELEMENT maxsites (#PCDATA)*>\n-<!ELEMENT csites (#PCDATA)*>\n-<!ELEMENT strands (#PCDATA)*>\n-<!ELEMENT priors_file (#PCDATA)*>\n-<!ELEMENT reason_for_stopping (#PCDATA)*>\n-<!ELEMENT back_order (#PCDATA)*>\n-<!ELEMENT background_frequencies (alphabet_array)>\n-<!ATTLIST background_frequencies source CDATA #REQUIRED>\n-\n-<!-- Motif elements -->\n-<!ELEMENT motifs (motif*)>\n-<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>\n-<!ATTLIST motif id ID #REQUIRED\n- name CDATA #REQUIRED\n- alt CDATA ""\n- width CDATA #REQUIRED\n- sites CDATA #REQUIRED\n- llr CDATA #REQUIRED\n- ic CDATA #REQUIRED\n- re CDATA #REQUIRED\n- bayes_threshold CDATA #REQUIRED\n- e_value CDATA #REQUIRED\n- elapsed_time CDATA #REQUIRED\n- url CDATA ""\n->\n-<!ELEMENT scores (alphabet_matrix)>\n-<!ELEMENT probabilities (alphabet_matrix)>\n-<!ELEMENT regular_expression (#PCDATA)*>\n-\n-<!-- Contributing site elements -->\n-<!-- Contributing sites are motif occurences found during the motif discovery phase -->\n-<!ELEMENT contributing_sites (contributing_site*)>\n-<!ELEMENT contributing_site (left_flank, site, right_flank)>\n-<!ATTLIST contributing_site sequence_id IDREF #REQUIRED\n- position CDATA #REQUIRED\n- strand (plus|minus|none) \'none\'\n- pvalue CDATA #REQUIRED\n->\n <!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->\n <!ELEMENT left_flank (#PCDATA)>\n <!-- The site contains the sequence for the motif instance -->\n <!ELEMENT site (letter_ref*)>\n <!-- The right_flank contains the sequence for '..b'="none" position="12" pvalue="3.06e-05"/>\n-</scanned_sites>\n <scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/>\n-</scanned_sites>\n <scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_7" pvalue="1.81e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="4.54e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_9" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="3.41e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_11" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="16" pvalue="8.67e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_12" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="18" pvalue="8.67e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_13" pvalue="2.01e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="5.01e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_14" pvalue="8.11e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="19" pvalue="2.03e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_15" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="21" pvalue="8.67e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_16" pvalue="2.71e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="22" pvalue="6.78e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_18" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="37" pvalue="3.82e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_19" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="9" pvalue="3.41e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_20" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="1.59e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_21" pvalue="1.60e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="7" pvalue="4.00e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_22" pvalue="4.83e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="2" pvalue="1.21e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_23" pvalue="2.43e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="6.06e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_24" pvalue="4.26e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="1.06e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_25" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="36" pvalue="3.41e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_28" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="1.59e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_29" pvalue="1.61e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="30" pvalue="4.02e-05"/>\n-</scanned_sites>\n-</scanned_sites_summary>\n </MEME>\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/meme_output_test2.html --- a/test-data/meme_output_test2.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test2.html Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -7,7931 +7,21 @@\n // @JSON_VAR data\n var data = {\n "program": "MEME",\n- "version": "4.12.0",\n- "release": "Tue Jun 27 16:22:50 2017 -0700",\n+ "version": "5.0.5",\n+ "release": "Mon Mar 18 20:12:19 2019 -0700",\n "stop_reason": "Stopped because requested number of motifs (1) found.",\n "cmd": [\n- "meme", "meme_input_1.fasta", "-o", "meme_test2_out", "-nostatus",\n- "-maxsize", "1000000", "-sf", "Galaxy_FASTA_Input", "-dna", "-mod",\n- "zoops", "-nmotifs", "1", "-wnsites", "0.8", "-minw", "8", "-maxw",\n- "50", "-wg", "11", "-ws", "1", "-maxiter", "50", "-distance",\n- "0.001", "-prior", "dirichlet", "-b", "0.01", "-plib",\n- "prior30.plib", "-spmap", "uni", "-spfuzz", "0.5"\n+ "meme",\n+ "-o",\n+ "-nostatus", "-maxsize", "1000000", "-sf", "Galaxy_FASTA_Input",\n+ "-dna", "-mod", "zoops", "-nmotifs", "1", "-wnsites", "0.8",\n+ "-minw", "8", "-maxw", "50", "-wg", "11", "-ws", "1", "-maxiter",\n+ "50", "-distance", "0.001", "-prior", "dirichlet", "-b", "0.01",\n+ "-plib",\n+ "-spmap", "uni", "-spfuzz", "0.5"\n ],\n- "options": {\n- "mod": "zoops",\n- "revcomp": false,\n- "nmotifs": 1,\n- "minw": 8,\n- "maxw": 50,\n- "minsites": 2,\n- "maxsites": 30,\n- "wnsites": 0.8,\n- "spmap": "uni",\n- "spfuzz": 0.5,\n- "maxwords": -1,\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- },\n- "alphabet": {\n- "name": "DNA",\n- "like": "dna",\n- "ncore": 4,\n- "symbols": [\n- {\n- "symbol": "A",\n- "name": "Adenine",\n- "colour": "CC0000",\n- "complement": "T"\n- }, {\n- "symbol": "C",\n- "name": "Cytosine",\n- "colour": "0000CC",\n- "complement": "G"\n- }, {\n- "symbol": "G",\n- "name": "Guanine",\n- "colour": "FFB300",\n- "complement": "C"\n- }, {\n- "symbol": "T",\n- "aliases": "U",\n- "name": "Thymine",\n- "colour": "008000",\n- "complement": "A"\n- }, {\n- "symbol": "N",\n- "aliases": "X.",\n- "name": "Any base",\n- "equals": "ACGT"\n- }, {\n- "symbol": "V",\n- "name": "Not T",\n- "equals": "ACG"\n- }, {\n- "symbol": "H",\n- "name": "Not G",\n- "equals": "ACT"\n- }, {\n- "symbol": "D",\n- "name": "Not C",\n- "equals": "AGT"\n- }, {\n- "symbol": "B",\n- "name": "Not A",\n- "equals": "CGT"\n- }, {\n- "symbol": "M",\n- "name": "Amino",\n- "equals": "AC"\n- }, {\n- "symbol": "R",\n- "name": "Purine",\n- "equals": "AG"\n- }, {\n- "symbol": "W",\n- "name": "Weak",\n- "equals": "AT"\n- }, {\n- "symbol": "S",\n- "name": "Strong",\n- "equals": "CG"\n- }, {\n- "symbol": "Y",\n- "name": "Pyrimidine",\n- "equals": "CT"\n- }, {\n- "symbol": "K",\n- "name": "Keto",\n- "equals": "GT"\n- }\n- ]\n- },\n- "background": {\n- "freqs": [0.294, 0.231, 0.257, 0.217]\n- },\n- "sequence_db": {\n- "source": "Galaxy_FASTA_Input",\n- "psp_source": "prior30.plib",\n- "fre'..b' <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>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- $("opt_strand").className = (meme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");\n- $("opt_nmotifs").textContent = data.options.nmotifs;\n- $("opt_evt").textContent = (typeof data.options.evt === "number" ? data.options.evt : "no limit");\n- $("opt_minw").textContent = data.options.minw;\n- $("opt_maxw").textContent = data.options.maxw;\n- $("opt_minsites").textContent = data.options.minsites;\n- $("opt_maxsites").textContent = data.options.maxsites;\n- $("opt_wnsites").textContent = data.options.wnsites;\n- $("opt_spmap").className = data.options.spmap;\n- $("opt_spfuzz").textContent = data.options.spfuzz;\n- $("opt_prior").className = data.options.prior;\n- $("opt_b").textContent = data.options.b;\n- $("opt_maxiter").textContent = data.options.maxiter;\n- $("opt_distance").textContent = data.options.distance;\n- $("opt_wg").textContent = data.options.wg;\n- $("opt_ws").textContent = data.options.ws;\n- $("opt_noendgaps").className = (data.options.noendgaps ? "on" : "off");\n- $("opt_substring").className = (data.options.substring ? "on" : "off");\n- }\n- </script>\n- </div>\n- <!-- list information on this program -->\n- <div id="info_sec" class="bar">\n- <div class="subsection">\n- <h5 id="version">MEME version</h5>\n- <span id="ins_version"></span> \n- (Release date: <span id="ins_release"></span>)<br>\n- </div>\n- <script>\n- $("ins_version").innerHTML = data["version"];\n- $("ins_release").innerHTML = data["release"];\n- </script>\n- <div class="subsection">\n- <h5 id="reference">Reference</h5>\n- <span class="citation">\n- Timothy L. Bailey and Charles Elkan, \n- "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", \n- <em>Proceedings of the Second International Conference on Intelligent Systems \n- for Molecular Biology</em>, pp. 28-36, AAAI Press, Menlo Park, California, 1994. \n- </span>\n- </div>\n- <div class="subsection">\n- <h5 id="command">Command line</h5>\n- <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly">\n- </textarea>\n- <script>$("cmd").value = data["cmd"].join(" ");</script>\n- </div>\n- </div>\n- \n- </body>\n-</html>\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/meme_output_test2.txt --- a/test-data/meme_output_test2.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test2.txt Wed Dec 11 18:04:34 2019 -0500 |
| [ |
| b'@@ -1,88 +1,36 @@\n ********************************************************************************\n MEME - Motif discovery tool\n-********************************************************************************\n-MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700)\n-\n-For further information on how to interpret these results or to get\n-a copy of the MEME software please access http://meme-suite.org .\n-\n-This file may be used as input to the MAST algorithm for searching\n-sequence databases for matches to groups of motifs. MAST is available\n-for interactive use and downloading at http://meme-suite.org .\n-********************************************************************************\n-\n-\n-********************************************************************************\n+MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)\n REFERENCE\n-********************************************************************************\n-If you use this program in your research, please cite:\n-\n-Timothy L. Bailey and Charles Elkan,\n-"Fitting a mixture model by expectation maximization to discover\n-motifs in biopolymers", Proceedings of the Second International\n-Conference on Intelligent Systems for Molecular Biology, pp. 28-36,\n-AAAI Press, Menlo Park, California, 1994.\n-********************************************************************************\n-\n-\n-********************************************************************************\n TRAINING SET\n-********************************************************************************\n-DATAFILE= Galaxy_FASTA_Input\n+PRIMARY SEQUENCES= Galaxy_FASTA_Input\n+CONTROL SEQUENCES= --none--\n ALPHABET= ACGT\n Sequence name Weight Length Sequence name Weight Length \n ------------- ------ ------ ------------- ------ ------ \n chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 \n-chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 \n-chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 \n-chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 \n-chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 \n-chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 \n-chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 \n-chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 \n-chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 \n-chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 \n-chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 \n-chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 \n-chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 \n-chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 \n-chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 \n-********************************************************************************\n-\n-********************************************************************************\n COMMAND LINE SUMMARY\n-********************************************************************************\n-This information can also be useful in the event you wish to report a\n-problem with the MEME software.\n-\n-command: meme meme_input_1.fasta -o meme_test2_out -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib prior30.plib -spmap uni -spfuzz 0.5 \n-\n model: mod= zoops nmotifs= 1 evt= inf\n-object function= E-value of product of p-values\n+objective function: em= E-value of product of p-values\n+ starts= E-value of product of p-values\n+strands: +\n width: minw'..b'y 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-\n-\n-\n-\n-Time 0.38 secs.\n-\n-********************************************************************************\n-\n-\n-********************************************************************************\n SUMMARY OF MOTIFS\n-********************************************************************************\n-\n---------------------------------------------------------------------------------\n \tCombined block diagrams: non-overlapping sites with p-value < 0.0001\n---------------------------------------------------------------------------------\n SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM\n-------------- ---------------- -------------\n chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)]\n-chr21_26934381_26934431_ 1.57e-03 27_[+1(3.93e-05)]_12\n-chr21_28217753_28217803_ 1.00e-01 50\n-chr21_31710037_31710087_ 2.49e-03 14_[+1(6.24e-05)]_25\n-chr21_31744582_31744632_ 1.22e-03 12_[+1(3.04e-05)]_27\n-chr21_31768316_31768366_ 1.47e-03 [+1(3.67e-05)]_39\n-chr21_31914206_31914256_ 6.45e-04 15_[+1(1.61e-05)]_24\n-chr21_31933633_31933683_ 2.26e-03 4_[+1(5.65e-05)]_35\n-chr21_31962741_31962791_ 3.37e-02 50\n-chr21_31964683_31964733_ 1.95e-04 13_[+1(4.86e-06)]_26\n-chr21_31973364_31973414_ 5.73e-02 50\n-chr21_31992870_31992920_ 5.52e-04 16_[+1(1.38e-05)]_23\n-chr21_32185595_32185645_ 2.59e-04 18_[+1(6.48e-06)]_21\n-chr21_32202076_32202126_ 1.10e-04 13_[+1(2.74e-06)]_26\n-chr21_32253899_32253949_ 7.78e-04 17_[+1(1.95e-05)]_22\n-chr21_32410820_32410870_ 5.52e-04 21_[+1(1.38e-05)]_18\n-chr21_36411748_36411798_ 2.85e-03 22_[+1(7.15e-05)]_17\n-chr21_37838750_37838800_ 1.90e-02 50\n-chr21_45705687_45705737_ 8.63e-04 37_[+1(2.16e-05)]_2\n-chr21_45971413_45971463_ 1.95e-04 9_[+1(4.86e-06)]_30\n-chr21_45978668_45978718_ 2.59e-04 4_[+1(6.48e-06)]_35\n-chr21_45993530_45993580_ 1.95e-04 7_[+1(4.86e-06)]_32\n-chr21_46020421_46020471_ 7.78e-04 2_[+1(1.95e-05)]_37\n-chr21_46031920_46031970_ 8.89e-05 15_[+1(2.22e-06)]_24\n-chr21_46046964_46047014_ 1.80e-05 12_[+1(4.51e-07)]_27\n-chr21_46057197_46057247_ 1.95e-04 36_[+1(4.86e-06)]_3\n-chr21_46086869_46086919_ 5.54e-03 50\n-chr21_46102103_46102153_ 5.54e-03 50\n-chr21_47517957_47518007_ 2.59e-04 32_[+1(6.48e-06)]_7\n-chr21_47575506_47575556_ 1.22e-03 30_[+1(3.04e-05)]_9\n---------------------------------------------------------------------------------\n-\n-********************************************************************************\n-\n-\n-********************************************************************************\n Stopped because requested number of motifs (1) found.\n-********************************************************************************\n-\n-CPU: ThinkPad-T450s\n-\n-********************************************************************************\n' |
| b |
| diff -r b48e673af4e8 -r ff2f53a32d0e test-data/meme_output_test2.xml --- a/test-data/meme_output_test2.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test2.xml Wed Dec 11 18:04:34 2019 -0500 |
| b |
| b'@@ -10,975 +10,73 @@\n <!ATTLIST MEME \n version CDATA #REQUIRED\n release CDATA #REQUIRED\n->\n <!-- Training-set elements -->\n <!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>\n-<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED>\n+<!ATTLIST training_set primary_sequences CDATA #REQUIRED primary_count CDATA #REQUIRED primary_positions CDATA #REQUIRED\n+ control_sequences CDATA "" control_count CDATA "" control_positions CDATA "">\n <!ELEMENT alphabet (letter*)>\n <!ATTLIST alphabet name CDATA #REQUIRED>\n-<!ELEMENT ambigs (letter*)>\n-<!ELEMENT letter EMPTY>\n-<!ATTLIST letter id ID #REQUIRED>\n-<!ATTLIST letter symbol CDATA #REQUIRED>\n-<!ATTLIST letter equals CDATA #IMPLIED>\n-<!ATTLIST letter aliases CDATA #IMPLIED>\n-<!ATTLIST letter complement CDATA #IMPLIED>\n-<!ATTLIST letter name CDATA #IMPLIED>\n-<!ATTLIST letter colour CDATA #IMPLIED>\n-<!ELEMENT sequence EMPTY>\n-<!ATTLIST sequence id ID #REQUIRED\n- name CDATA #REQUIRED\n- length CDATA #REQUIRED\n- weight CDATA #REQUIRED\n->\n <!ELEMENT letter_frequencies (alphabet_array)>\n-\n <!-- Model elements -->\n <!ELEMENT model (\n command_line,\n host,\n type,\n nmotifs,\n- evalue_threshold,\n- object_function,\n- spfun,\n- min_width,\n- max_width,\n- wg,\n- ws,\n- endgaps,\n- minsites,\n- maxsites,\n- wnsites,\n- spmap,\n- spfuzz,\n- prior,\n- beta,\n- maxiter,\n- distance,\n- num_sequences,\n- num_positions,\n- seed,\n- hsfrac,\n- maxwords,\n- maxsize,\n- csites,\n- strands,\n- priors_file,\n- reason_for_stopping,\n- back_order,\n- background_frequencies\n )>\n <!ELEMENT command_line (#PCDATA)*>\n-<!ELEMENT host (#PCDATA)*>\n-<!ELEMENT type (#PCDATA)*>\n-<!ELEMENT nmotifs (#PCDATA)*>\n-<!ELEMENT evalue_threshold (#PCDATA)*>\n-<!ELEMENT object_function (#PCDATA)*>\n-<!ELEMENT spfun (#PCDATA)*>\n-<!ELEMENT min_width (#PCDATA)*>\n-<!ELEMENT max_width (#PCDATA)*>\n-<!ELEMENT wg (#PCDATA)*>\n-<!ELEMENT ws (#PCDATA)*>\n-<!ELEMENT endgaps (#PCDATA)*>\n-<!ELEMENT minsites (#PCDATA)*>\n-<!ELEMENT maxsites (#PCDATA)*>\n-<!ELEMENT wnsites (#PCDATA)*>\n-<!ELEMENT spmap (#PCDATA)*>\n-<!ELEMENT spfuzz (#PCDATA)*>\n-<!ELEMENT prior (#PCDATA)*>\n-<!ELEMENT beta (#PCDATA)*>\n-<!ELEMENT maxiter (#PCDATA)*>\n-<!ELEMENT distance (#PCDATA)*>\n-<!ELEMENT num_sequences (#PCDATA)*>\n-<!ELEMENT num_positions (#PCDATA)*>\n-<!ELEMENT seed (#PCDATA)*>\n-<!ELEMENT hsfrac (#PCDATA)*>\n-<!ELEMENT maxwords (#PCDATA)*>\n-<!ELEMENT maxsites (#PCDATA)*>\n-<!ELEMENT csites (#PCDATA)*>\n-<!ELEMENT strands (#PCDATA)*>\n-<!ELEMENT priors_file (#PCDATA)*>\n-<!ELEMENT reason_for_stopping (#PCDATA)*>\n-<!ELEMENT back_order (#PCDATA)*>\n-<!ELEMENT background_frequencies (alphabet_array)>\n-<!ATTLIST background_frequencies source CDATA #REQUIRED>\n-\n-<!-- Motif elements -->\n <!ELEMENT motifs (motif*)>\n <!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>\n-<!ATTLIST motif id ID #REQUIRED\n- name CDATA #REQUIRED\n- alt CDATA ""\n- width CDATA #REQUIRED\n- sites CDATA #REQUIRED\n- llr CDATA #REQUIRED\n- ic CDATA #REQUIRED\n- re CDATA #REQUIRED\n- bayes_threshold CDATA #REQUIRED\n- e_value CDATA #REQUIRED\n- elapsed_time CDATA #REQUIRED\n- url CDATA ""\n->\n-<!ELEMENT scores (alphabet_matrix)>\n-<!ELEMENT probabilities (alphabet_matrix)>\n-<!ELEMENT regular_expression (#PCDATA)*>\n-\n-<!-- Contributing site elements -->\n-<!-- Contributing sites are motif occurences found during the motif discovery phase -->\n-<!ELEMENT contributing_sites (contributing_site*)>\n-<!ELEMENT contributing_site (left_flank, site, right_flank)>\n-<!ATTLIST contributing_site sequence_id IDREF #REQUIRED\n- position CDATA #REQUIRED\n- strand (plus|minus|none) \'none\'\n- pvalue CDATA #REQUIRED\n->\n <!-- The left_flank contains the sequence for 10 bases to the l'..b'="plus" position="12" pvalue="3.04e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>\n-<scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>\n-</scanned_sites>\n-<scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>\n-</scanned_sites>\n-</scanned_sites_summary>\n </MEME>\n' |