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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa |
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added:
test-data/dreme1.html test-data/dreme1.txt test-data/dreme1.xml test-data/dreme2.html test-data/dreme2.txt test-data/dreme_test_sites.fa |
| b |
| diff -r a0fa4efeeee3 -r 793225b11202 test-data/dreme1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme1.html Wed Apr 25 12:13:08 2018 -0400 |
| [ |
| b'@@ -0,0 +1,6199 @@\n+<!DOCTYPE HTML>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <title>DREME</title>\n+ <script>\n+ // @JSON_VAR data\n+ var data = {\n+ "program": "dreme",\n+ "version": "4.11.2",\n+ "release": "Thu May 05 14:58:55 2016 -0700",\n+ "cmd": [\n+ "dreme", "-o", "./output", "-p",\n+ "/tmp/tmpijN1y0/files/000/dataset_1.dat", "-norc", "-rna", "-s",\n+ "1"\n+ ],\n+ "options": {\n+ "revcomp": false,\n+ "ngen": 100,\n+ "add_pv_thresh": 0.01,\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": "dataset 1",\n+ "file": "/tmp/tmpijN1y0/files/000/dataset_1.dat",\n+ "lmod": "Tue Apr 24 13:55:48 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": "MEME",\n+ "len": 6,\n+ "nsites": 459,\n+ "evalue": "1.2e-013",\n+ "p": 387,\n+ "n": 210,\n+ "pvalue": "2.6e-018",\n+ "unerased_evalue": "1.2e-013",\n+ "pwm": [\n+ [0.000000, 0.000000, 0.000000, 1.000000], \n+ [0.000000, 0.000000, 0.000000, 1.000000], \n+ [0.000000, 0.294118, 0.000000, 0.705882], \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": "8.1e-003"\n+ }, {\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' |
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| diff -r a0fa4efeeee3 -r 793225b11202 test-data/dreme1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme1.txt Wed Apr 25 12:13:08 2018 -0400 |
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| @@ -0,0 +1,102 @@ +# DREME 4.12.0 +# command: dreme -oc dreme_out -rna -norc -p dreme_test_sites.fa -e 0.05 -mink 3 -maxk 8 +# positives: 1000 from dreme_test_sites.fa (Thu Apr 19 19:09:45 CEST 2018) +# negatives: 1000 from shuffled positives +# host: ThinkPad-T450s +# when: Thu Apr 19 19:11:17 CEST 2018 + +MEME version 4.12.0 + +ALPHABET "RNA" RNA-LIKE +A "Adenine" CC0000 +C "Cytosine" 0000CC +G "Guanine" FFB300 +U "Uracil" 008000 +N "Any base" = ACGU +X = ACGU +. = ACGU +V "Not U" = ACG +H "Not G" = ACU +D "Not C" = AGU +B "Not A" = CGU +M "Amino" = AC +R "Purine" = AG +W "Weak" = AU +S "Strong" = CG +Y "Pyrimidine" = CU +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 +0.000000 0.294118 0.000000 0.705882 +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 +1.000000 0.000000 0.000000 0.000000 +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 +0.000000 0.000000 0.000000 1.000000 +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: 13.45 seconds |
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| diff -r a0fa4efeeee3 -r 793225b11202 test-data/dreme1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme1.xml Wed Apr 25 12:13:08 2018 -0400 |
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| @@ -0,0 +1,32 @@ +<dreme version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> + <model> + <command_line>dreme -oc dreme_out -rna -norc -p dreme_test_sites.fa -e 0</command_line> + <positives name="dreme test sites" count="1000" file="dreme_test_sites.fa" last_mod_date="Thu Apr 19 19:09:45 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"/> + <letter id="C" symbol="C" name="Cytosine" colour="0000CC"/> + <letter id="G" symbol="G" name="Guanine" colour="FFB300"/> + <letter id="U" symbol="U" aliases="T" name="Uracil" colour="008000"/> + <letter id="N" symbol="N" aliases="X." equals="ACGU" name="Any base"/> + <letter id="V" symbol="V" equals="ACG" name="Not U"/> + <letter id="H" symbol="H" equals="ACU" name="Not G"/> + <letter id="D" symbol="D" equals="AGU" name="Not C"/> + <letter id="B" symbol="B" equals="CGU" name="Not A"/> + <letter id="M" symbol="M" equals="AC" name="Amino"/> + <letter id="R" symbol="R" equals="AG" name="Purine"/> + <letter id="W" symbol="W" equals="AU" name="Weak"/> + <letter id="S" symbol="S" equals="CG" name="Strong"/> + <letter id="Y" symbol="Y" equals="CU" name="Pyrimidine"/> + <letter id="K" symbol="K" equals="GU" name="Keto"/> + </alphabet> + <strands>none</strands> + <background A="0.221" C="0.245" G="0.221" U="0.312" from="dataset"/> + <stop evalue="0"/> + <ngen>100</ngen> + <add_pv_thresh>0.01</add_pv_thresh> + <seed>1</seed> + <host>ThinkPad-T450s</host> + <when>Thu Apr 19 19:40:08 CEST 2018</when> + </model> + <motifs> |
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| diff -r a0fa4efeeee3 -r 793225b11202 test-data/dreme2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme2.html Wed Apr 25 12:13:08 2018 -0400 |
| [ |
| b'@@ -0,0 +1,6118 @@\n+<!DOCTYPE HTML>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <title>DREME</title>\n+ <script>\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+ "cmd": [\n+ "dreme", "-oc", "dreme_out_adv", "-rna", "-norc", "-p",\n+ "dreme_test_sites.fa", "-e", "0.00001", "-mink", "4", "-maxk", "10"\n+ ],\n+ "options": {\n+ "revcomp": false,\n+ "ngen": 100,\n+ "add_pv_thresh": 0.01,\n+ "seed": 1,\n+ "stop": {\n+ "evalue": "1e-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 19 19:09:45 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+ "len": 6,\n+ "nsites": 459,\n+ "evalue": "3.3e-013",\n+ "p": 387,\n+ "n": 210,\n+ "pvalue": "2.6e-018",\n+ "unerased_evalue": "3.3e-013",\n+ "pwm": [\n+ [0.000000, 0.000000, 0.000000, 1.000000], \n+ [0.000000, 0.000000, 0.000000, 1.000000], \n+ [0.000000, 0.294118, 0.000000, 0.705882], \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+ '..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 a0fa4efeeee3 -r 793225b11202 test-data/dreme2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme2.txt Wed Apr 25 12:13:08 2018 -0400 |
| b |
| @@ -0,0 +1,68 @@ +# DREME 4.12.0 +# command: dreme -oc dreme_out_adv -rna -norc -p dreme_test_sites.fa -e 0.00001 -mink 4 -maxk 10 +# positives: 1000 from dreme_test_sites.fa (Thu Apr 19 19:09:45 CEST 2018) +# negatives: 1000 from shuffled positives +# host: ThinkPad-T450s +# when: Tue Apr 24 18:44:36 CEST 2018 + +MEME version 4.12.0 + +ALPHABET "RNA" RNA-LIKE +A "Adenine" CC0000 +C "Cytosine" 0000CC +G "Guanine" FFB300 +U "Uracil" 008000 +N "Any base" = ACGU +X = ACGU +. = ACGU +V "Not U" = ACG +H "Not G" = ACU +D "Not C" = AGU +B "Not A" = CGU +M "Amino" = AC +R "Purine" = AG +W "Weak" = AU +S "Strong" = CG +Y "Pyrimidine" = CU +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 +0.000000 0.294118 0.000000 0.705882 +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: 18.17 seconds |
| b |
| diff -r a0fa4efeeee3 -r 793225b11202 test-data/dreme_test_sites.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreme_test_sites.fa Wed Apr 25 12:13:08 2018 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\n+>U2AF2_K562_rep02_1\n+UCUACACAUAGGGUGUUCCUGAAAAGCCCCAUAGUGAUUGAGUCUUCAAAACCACCGAUUC\n+>U2AF2_K562_rep02_2\n+UUGGAUAGCGGAAGCCCUGACCAGGCAUGGAGUAUCUCACAAAGUAGACGAUUCCUCUGGG\n+>U2AF2_K562_rep02_3\n+GGUUUCGGUCUAAGUACCACCCAGAUGAGGUGGGGAAGCGUCGGCAGGAGGCCCGGGGGGC\n+>U2AF2_K562_rep02_4\n+AAACAGGGUUUGUGGAUGCACUUAGAUGUUUGCAAUGAGCACUGUGGCUGGCAUGCCCCAG\n+>U2AF2_K562_rep02_5\n+UCCCAUUGUUUCUGCAGAGGCAGUUGGUGUCACCAGCCAGCGACCAGUGUUUUGUCCUUUU\n+>U2AF2_K562_rep02_6\n+UUCUACCCUCUCUAACUCCUCCCAGCAGCAAAAGGGAGACACUUCAGCUGGAACAAAAUAG\n+>U2AF2_K562_rep02_7\n+UUCUACCCUCUCUAACUCCUCCCAGCAGCAAAAGGGAGACACUUCAGCUGGAACAAAAUAG\n+>U2AF2_K562_rep02_8\n+UUUUCUCCCUUCCACCCACACCCUGCAGCGUCGAGGUCCUCAGCGAUCAGUUGAUGUAAUA\n+>U2AF2_K562_rep02_9\n+GGCAGGGGAAGUGGGGAUGGCAGGACAUGGAUGGCCCUUGAGGCAUUGGCUCUGGGUGUCA\n+>U2AF2_K562_rep02_10\n+GCAGGGGAAGUGGGGAUGGCAGGACAUGGAUGGCCCUUGAGGCAUUGGCUCUGGGUGUCAU\n+>U2AF2_K562_rep02_11\n+UUAGUCUUUCCAUCUACAGCCCACUGGCACUCCAGGCACCUACCUACUUCAAACAAGCUCA\n+>U2AF2_K562_rep02_12\n+UUUCUCUUUUCCUUCCACAGGGGACCGUGAUUAGGGUAUUUUCCAUUCCAGAAGGACAAAA\n+>U2AF2_K562_rep02_13\n+AUAACUGUUUUGUCUUUCCCUCCCCCGCUUCGUUCCCAGGUUUCGGUCUAAGUACCACCCA\n+>U2AF2_K562_rep02_14\n+UUUCAGAGAACGUUUGUCUGCCUGAUGAGAGCCACUUGGGUUAAGAAACUACCUGUGAAUA\n+>U2AF2_K562_rep02_15\n+AUGCUUUGCAAUUGCAGCUCCUUUAUGUCUCCAAAUGAUACAAGAAGACCCGAGAAAGUGG\n+>U2AF2_K562_rep02_16\n+UUUGCAAUUUUGCCUAGGGCCCUGGUGGUGGCAACCGCCUGUGUGCCACUGAAAAUCGUGC\n+>U2AF2_K562_rep02_17\n+UUGCAAUUUUGCCUAGGGCCCUGGUGGUGGCAACCGCCUGUGUGCCACUGAAAAUCGUGCC\n+>U2AF2_K562_rep02_18\n+CUAAUUUUUAAAAAGCAGCCUCUGGAGCCAGCCAUGUUUGGCACUGAAUCUUCAUGUAAGU\n+>U2AF2_K562_rep02_19\n+UCUAAUUUUUAAAAAGCAGCCUCUGGAGCCAGCCAUGUUUGGCACUGAAUCUUCAUGUAAG\n+>U2AF2_K562_rep02_20\n+UUUCUGUCUUCUCCUCUCUUCCUUUACACAAACUUAAACAGAAUGGAAAUGAAAACCAAGG\n+>U2AF2_K562_rep02_21\n+AAACAGUUUCAGCUCCUGGCAUCAGCUCUAUUCAAAUCUGGUUCAGAUUUUACAGCUCUGG\n+>U2AF2_K562_rep02_22\n+UUCUCUCUCUUCCCCUGGCUCCCUCAAGGUGAACAGCCAUAUACCAGGAAUAGGAUACCAG\n+>U2AF2_K562_rep02_23\n+UAUAUCCUUAGUGCAGGCUGUGGAAGAACAGGUGCCAUUUGUGCCAUAGAUUAUACGUGGA\n+>U2AF2_K562_rep02_24\n+UCCCUAAUUCUUCACCUCCCCCUCCUCUGCUGCCUCCUUGCUCUCCUCGCAGGUCAAGUUU\n+>U2AF2_K562_rep02_25\n+AUUGUUACUCCCAGGUGCCUUCGAAACAUCUGCAAGUUUUUAGUCUUGCUCAUCCCACUCU\n+>U2AF2_K562_rep02_26\n+CACAUUUUUUAAAAGGGCAAGUACAGGAGCAACUGCUGCUACCCAGAAAAAUGUGUGUAUU\n+>U2AF2_K562_rep02_27\n+CACAUUUUUUAAAAGGGCAAGUACAGGAGCAACUGCUGCUACCCAGAAAAAUGUGUGUAUU\n+>U2AF2_K562_rep02_28\n+AUUCCGUAGGUUCUAAUCUGUUCUCCCUCCUCCUCAACGUAAGUACACAGUGGAUACCCUC\n+>U2AF2_K562_rep02_29\n+UAUUCCGUAGGUUCUAAUCUGUUCUCCCUCCUCCUCAACGUAAGUACACAGUGGAUACCCU\n+>U2AF2_K562_rep02_30\n+ACUAAAGUUUUUUUUCCUAGUGGUUAUCAUGAGACUUAUAUAAAACAUGUUGUAUCUUAAC\n+>U2AF2_K562_rep02_31\n+CCUCCUCUUUCUCCCUCCCUCCUUCAUUCCCUCCAUCCCUCUCUUAACAGCUUGAAGAUAA\n+>U2AF2_K562_rep02_32\n+CCUCCUCUUUCUCCCUCCCUCCUUCAUUCCCUCCAUCCCUCUCUUAACAGCUUGAAGAUAA\n+>U2AF2_K562_rep02_35\n+AUUUAUCCUCUUGCUUUUGCAUCUCAAAAUUUUAUCGCCUUGAAGACACGUUUCUAUGAAU\n+>U2AF2_K562_rep02_36\n+GUCAGAAGGUAGCAGGGGCUGGGGGUUGCAGGGGGAUGUUGAGAAGAAGUGGUCCUUUGGU\n+>U2AF2_K562_rep02_37\n+AGUCAGAAGGUAGCAGGGGCUGGGGGUUGCAGGGGGAUGUUGAGAAGAAGUGGUCCUUUGG\n+>U2AF2_K562_rep02_38\n+UUGCUUCUCCUUUCUUCCUUCCUUCCUGCCCAGGGCCUCAUCUUUGUGGUGGACAGUAAUG\n+>U2AF2_K562_rep02_39\n+UAGAGACUGUUUAUUUGUUUGGUGGCUGGGAUGGAACACAAGAUCUUGCUGACUUCUGGGC\n+>U2AF2_K562_rep02_40\n+CUUAGGUAUGCCGAGCAGACAGCUGGAGGAUCCCGGGGCAGGGACACCUAGCCCGGUGCGU\n+>U2AF2_K562_rep02_41\n+AUUCUCCUGGGUUUUUGGCAGAUGGUUGCAGUGGCAGGACCAAGGCCUAGUGAGCUAUAGC\n+>U2AF2_K562_rep02_42\n+GCAGAUGGUUGCAGUGGCAGGACCAAGGCCUAGUGAGCUAUAGCUAAAUCUACAGUGGGAU\n+>U2AF2_K562_rep02_43\n+CCCCGUGCCUUGCCUCCCCAGGCGUGUGACCCCCUGCCGCACGAGGAGGAGCCCUCUGAAG\n+>U2AF2_K562_rep02_44\n+UUUACCCCACUACUAGGUAAGGGGCCUGGAUACCAAGAAGUGACUGCUCAUCUAAUCCAUA\n+>U2AF2_K562_rep02_45\n+GAUGGUCAUUGUCCUCCAGAGCAGUGAUGGAGGAAAUACCAGCCCAGGAAGCAGCAGGGUC\n+>U2AF2_K562_rep02_46\n+AUGGUCAUUGUCCUCCAGAGCAGUGAUGGAGGAAAUACCAGCCCAGGAAGCAGCAGGGUCA\n+>U2AF2_K562_rep02_47\n+UAGGCCUGUGAGGCUGCCACACCCUGUGCCCCCGUGCCUUGCCUCCCCAGGCGUGUGACCC\n+>U2AF2_K562_rep02_48\n+CAGGUCUCUCCUUACGGGGCCAGGGCAAUUUCUUUUCGUUCUUGCCCGUGUUGAACUGGGC\n+>U2AF2_K562_rep02_49\n+UACUUCUCUUUCCCUGUCCCCAAAGCAGAUCGCCAAACUGAGGCAGCAACUACAAC'..b'UUUUGGUAGGAAACUCAACAGUGUAAAUUUGAUGGCCA\n+>U2AF2_K562_rep02_12274\n+UGAUUUUGUCCCCUAGAGCAAGGUCCGUGGUCCUGUCAGUGGAAGCCCGGAUAGCAUGAAU\n+>U2AF2_K562_rep02_12275\n+GGUGGGGUGGGGGCGGGGAGGGCUCCCGGGAGGCAAGUGGUCACGGUGAGAGUCACUGGGC\n+>U2AF2_K562_rep02_12276\n+UACCCAUUGCUUUUACUGAUUAGGUAUGAAUUUCAGCCCUUUAUUUCCUUCUAAUUUUGGA\n+>U2AF2_K562_rep02_12279\n+CCUCAUUUCACCCAGGAGGAAGGUGCAGCUCAGAGCUGUUACGACUAGUCAGAGAGAGCGA\n+>U2AF2_K562_rep02_12281\n+AUAAUUCUUACCUGCCUCCUUUCUCUUCCCGGACCUUCCUAAUUUGAAGAGGUGAUUUGGA\n+>U2AF2_K562_rep02_12286\n+UUUCUCUCCCUAAUCUUUUCUCCAAUCAGGCUUCAAUGUUAGCUGCAGAAAAUGACCCUUA\n+>U2AF2_K562_rep02_12287\n+UUUUUGUUUUUCAGCCCUGGUACCUGACAGUGUAAAGAAGGAGCUCCUACAAAGAAUAAGA\n+>U2AF2_K562_rep02_12292\n+UUUACCUGGGUAACAAUUUUACUUUUUACCACAGUCACCAAGGAGCUAGUUAGCUGGAUGA\n+>U2AF2_K562_rep02_12293\n+UAGUUUGCAGGUCGAAGUAAGAAGGAAACCAAAUAUUCUCUUAAGGCUGUCGAAGACAUGU\n+>U2AF2_K562_rep02_12299\n+UUUGUUUUUCUUUUCAGGUAUGGAACCCUUCAGAUCAAAGCUUACCAAUAAAUUCAGUAUG\n+>U2AF2_K562_rep02_12300\n+UUUGUUUUUCUUUUCAGGUAUGGAACCCUUCAGAUCAAAGCUUACCAAUAAAUUCAGUAUG\n+>U2AF2_K562_rep02_12302\n+CUCAUUUUUCUCUUGCCGCCGCCAUGUAAGAGGUAACUUUCACCUCCCGUCAUGAUUCUGA\n+>U2AF2_K562_rep02_12303\n+UUAUUUUUCUUAUUUAGGGAAGGUUACCGCCACCUCUCUGUAGGAAAUCAAGUGUACAUGA\n+>U2AF2_K562_rep02_12305\n+ACUUGCUAUCCUUCCCUUGCAGGAAGACACGUUUCAGCAGUAUGUAAGACCAGAGAUUAAC\n+>U2AF2_K562_rep02_12306\n+CUUGUGCAAUUUCCAGGUGAUGAACAGCCUCCUUCUAAAUCAUUGACCACAUUUCUUAUUC\n+>U2AF2_K562_rep02_12307\n+UUCUCUUUUUGUGCCAGGUCAUACUUUAAGGAGCCCAAGAGCUUUAUAACAUAACAAAAGA\n+>U2AF2_K562_rep02_12308\n+UUCUCUUUUUGUGCCAGGUCAUACUUUAAGGAGCCCAAGAGCUUUAUAACAUAACAAAAGA\n+>U2AF2_K562_rep02_12311\n+UCCCUUAAACUUUAUACCACCAGAAUACCAACAGAAGCUAAAUGUAGCAAAUGUGACUGCC\n+>U2AF2_K562_rep02_12312\n+AAAAUUAAGUUCUUUUAUUAGCUGGCCGUUCUCUCAUUAUCUCAAAUUUAUUUAAGUAUUU\n+>U2AF2_K562_rep02_12316\n+UUUUCUUCUUUGUAGCAUGGAGCAGAUCCAACUAAAAAGAACAGAGAUGGAAAUACACCUU\n+>U2AF2_K562_rep02_12317\n+CUUUUCUCUAGGUUAGUAACACUGAAGAAAUCACUUUUGAAGCAUUGAAGAAAGCAAUUGG\n+>U2AF2_K562_rep02_12318\n+UCAUAGCUCCUUCUCCCCCUGCUUCUUUCCCAAAUGAAUGAGUAUUUCUUUUAGAUAAAUU\n+>U2AF2_K562_rep02_12321\n+AUUAUUUUUUUGUGUUGGCCAGGAAGUGAACCCAGGUCAACUGCUUGGAAGGUGGCUAUGC\n+>U2AF2_K562_rep02_12322\n+ACAGGCCCAGACCUUCUCUUUCCCUUUCCAGCAGCCGGAGAAGUGCGACAACAACCAGUAC\n+>U2AF2_K562_rep02_12323\n+CCCACCGCCUUGACACCCCCACCCCCGCAGGGAAGCAGCUGGUGCACUACACAGCGCAGCC\n+>U2AF2_K562_rep02_12324\n+UUUUUUCAUUACAUUACAGGAAGCAGAAUCUGGUAAUAUAAGUCAAAAGUCUGAUGAAGAA\n+>U2AF2_K562_rep02_12325\n+GUUUUCUUUUUUCCCUUUCCCAGUUUGACUUUUGCCAUCUAGAGUUUGUAAAUUAAGUGGU\n+>U2AF2_K562_rep02_12326\n+CUUUCCCUUCCACAGCCCAGGGUCCGUCUGCAUUUUGUGGAGCUGGGCUCCGGCCCUGCUG\n+>U2AF2_K562_rep02_12334\n+UUUGACUUUGCUUUGCUUUUCCCCUUUUGUGUUUGCAGUUGAAUGGAGAGGUUUUCAUAUU\n+>U2AF2_K562_rep02_12335\n+AUAUUAAACUCUUCAGAAGGAAGUCACUGUGCAUAGCCAUCCCCUAAGAAGAGGGCAUUCC\n+>U2AF2_K562_rep02_12336\n+ACACUUCUGUUCCUUUGUCUGCAGGAGAGCUGGAGGUGUUUCAGAAAGAUGGGGAACGAAA\n+>U2AF2_K562_rep02_12337\n+UAAAACUGUGGUUUGCAAGCAGAAGGCGCUGGAACUGUUGCCCAAGGUGGAAGAGGUGGUG\n+>U2AF2_K562_rep02_12338\n+CUAUCCUUCUACCUCCACGCACGUUUUUUAAGGCAGCGGCAAAAGUAGUAGAAAGCAAAAG\n+>U2AF2_K562_rep02_12339\n+UCAGCUUUUUAAUUAAAUGAAGCCAAGUGGGAUUUGCAUAAAGUGAAUGUUUACCAUGAAG\n+>U2AF2_K562_rep02_12340\n+UUUUCCUCCUCAAUCUUCCUUUGCCCUACCUAUGUGUUACUAGAGAACAUUUCUACAAAUU\n+>U2AF2_K562_rep02_12341\n+UCUUUUUCCUUCCUCCCUCCCUGUCUCCCUCCCUCUCUGCCUCCCUCCCUCCCUCCCUCUU\n+>U2AF2_K562_rep02_12342\n+UGUCUUUUUUUCUUUAGUGCUCCAGACAAUGAAACAUCCAAAUCUGCUAAUCAAGAUACCU\n+>U2AF2_K562_rep02_12343\n+CUUUGUACCAAUAGGUAAUUUGUCGUCCAGAUGCUCUGCUAUAUGUGAAGUAUCAUUUUUC\n+>U2AF2_K562_rep02_12344\n+CUUUGUACCAAUAGGUAAUUUGUCGUCCAGAUGCUCUGCUAUAUGUGAAGUAUCAUUUUUC\n+>U2AF2_K562_rep02_12352\n+UUUUUCCUCUGAAUUUACAUGGAAGGAGCGGUAGAUGAUGAGACAUAUAAGAUCCUCACAU\n+>U2AF2_K562_rep02_12353\n+AGAUGCCACUGCCUCCUUUCCAUUGUCAGCUGGCGGGUGACGCGACUGUUGUUGCACUGGG\n+>U2AF2_K562_rep02_12354\n+AGAUGCCACUGCCUCCUUUCCAUUGUCAGCUGGCGGGUGACGCGACUGUUGUUGCACUGGG\n+>U2AF2_K562_rep02_12355\n+CUAACUUCUCUAGCCAAAUACAGAUAGUCUUUCCCACUGAGUGUCUGUCAACAACUAGAUU\n+>U2AF2_K562_rep02_12356\n+UCCCUGAUUCUUUUUCAAGGGCCGCUUGAAGAUGCCAUUGAAGAUGAGGAAGAAGAAUGUC\n+>U2AF2_K562_rep02_12357\n+AUUUUAAUUCUAGUCUAGGUGAUGGCUGCUCCUUUCCAACUUGCCUUGUUAACCAGGAUCC\n' |