1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/e448ba0e8843/ changeset: r5129:e448ba0e8843 user: kanwei date: 2011-02-25 20:58:35 summary: Update test-data files for meme 4.6.0 affected #: 4 files (2.8 KB)
--- a/test-data/meme/meme/meme_output_html_1.html Fri Feb 25 13:35:27 2011 -0500 +++ b/test-data/meme/meme/meme_output_html_1.html Fri Feb 25 14:58:35 2011 -0500 @@ -4,6 +4,8 @@ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>MEME</title><style type="text/css"> + + /* START INCLUDED FILE "meme.css" */ /* The following is the content of meme.css */ body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;}
@@ -13,6 +15,7 @@ padding: 0px; width: 12px; height: 13px; + cursor: pointer; background-image: url("help.gif"); background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAANAQMAAACn5x0BAAAAAXNSR0IArs4c6QAAAAZQTFRFAAAAnp6eqp814gAAAAF0Uk5TAEDm2GYAAAABYktHRACIBR1IAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH2gMJBQgGYqhNZQAAACZJREFUCNdj+P+BoUGAoV+AYeYEEGoWYGgTYGgRAAm2gRGQ8f8DAOnhC2lYnqs6AAAAAElFTkSuQmCC"); } @@ -123,8 +126,12 @@ padding:0px 10px; }
+ /* END INCLUDED FILE "meme.css" */ + </style><script type="text/javascript"> + + /* START INCLUDED FILE "motif_logo.js" */ //====================================================================== // start Alphabet object //====================================================================== @@ -337,7 +344,9 @@ //====================================================================== // start Pspm object //====================================================================== - function Pspm(pssm, name) { + function Pspm(pssm, name, ltrim, rtrim) { + if (ltrim === undefined) ltrim = 0; + if (rtrim === undefined) rtrim = 0; //variable prototype this.alph_length = 0; this.motif_length = 0; @@ -345,6 +354,8 @@ this.name = (typeof name == "string" ? name : ""); this.nsites = 0; this.evalue = 0; + this.ltrim = ltrim; + this.rtrim = rtrim; //function prototype this.copy = Pspm_copy; this.reverse_complement = Pspm_reverse_complement; @@ -352,10 +363,11 @@ this.get_stack_ic = Pspm_get_stack_ic; this.get_motif_length = Pspm_get_motif_length; this.get_alph_length = Pspm_get_alph_length; + this.get_left_trim = Pspm_get_left_trim; + this.get_right_trim = Pspm_get_right_trim; this.toString = Pspm_to_string; //construct var pspm_header = /letter-probability matrix:\s+alength=\s+(\d+)\s+w=\s+(\d+)(\s+nsites=\s+(\S+))?(\s+E=\s+(\S+))?\s*/; - var is_prob = /^((1(.0+)?)|(0(.\d+)?))$/; var is_empty = /^\s*$/; var lines = pssm.split(/\s*\n\s*/); var read_pssm = false; @@ -392,11 +404,14 @@ if (!parts.hasOwnProperty(part_index) || parts[part_index] === undefined) continue;
var prob = parts[part_index]; - if (!is_prob.test(prob)) continue; if (col_num >= this.alph_length) { throw "TOO_MANY_COLS"; } this.pspm[line_num][col_num] = (+prob); + //check the probability is within bounds + if (this.pspm[line_num][col_num] > 1 || this.pspm[line_num][col_num] < 0) { + throw "NUM_NOT_PROB"; + } col_num++; } if (col_num != this.alph_length) { @@ -417,6 +432,11 @@ //so far only a shallow copy, need to copy everything clone.alph_length = (0+this.alph_length); clone.motif_length = (0+this.motif_length); + clone.name = (""+this.name); + clone.nsites = (0+this.nsites); + clone.evalue = (0+this.evalue); + clone.ltrim = (0+this.ltrim); + clone.rtrim = (0+this.rtrim); clone.pspm = new Array(this.motif_length); for (row = 0; row < this.motif_length; row++) { clone.pspm[row] = new Array(this.alph_length); @@ -460,6 +480,10 @@ row[c_index] = row[g_index]; row[g_index] = temp; } + //swap triming + var temp_trim = this.ltrim; + this.ltrim = this.rtrim; + this.rtrim = temp_trim; //note that ambigs are ignored because they don't effect motifs return this; //allow function chaining... } @@ -515,6 +539,14 @@ return this.alph_length; }
+ function Pspm_get_left_trim() { + return this.ltrim; + } + + function Pspm_get_right_trim() { + return this.rtrim; + } + function Pspm_to_string() { var str = ""; for (row_index in this.pspm) { @@ -1036,6 +1068,62 @@ pos = pos - sym_height; } } + + function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) { + var x, y, len, i; + var dx = x2 - x1; + var dy = y2 - y1; + var tlen = Math.pow(dx*dx + dy*dy, 0.5); + var theta = Math.atan2(dy,dx); + var mulx = Math.cos(theta); + var muly = Math.sin(theta); + var lx = []; + var ly = []; + for (i = 0; i < pattern; ++i) { + lx.push(pattern[i] * mulx); + ly.push(pattern[i] * muly); + } + i = start; + x = x1; + y = y1; + len = 0; + ctx.beginPath(); + while (len + pattern[i] < tlen) { + ctx.moveTo(x, y); + x += lx[i]; + y += ly[i]; + ctx.lineTo(x, y); + len += pattern[i]; + i = (i + 1) % pattern.length; + x += lx[i]; + y += ly[i]; + len += pattern[i]; + i = (i + 1) % pattern.length; + } + if (len < tlen) { + ctx.moveTo(x, y); + x += mulx * (tlen - len); + y += muly * (tlen - len); + ctx.lineTo(x, y); + } + ctx.stroke(); + } + + function draw_trim_background(ctx, metrics, pspm, offset) { + var lwidth = metrics.stack_width * pspm.get_left_trim(); + var rwidth = metrics.stack_width * pspm.get_right_trim(); + var mwidth = metrics.stack_width * pspm.get_motif_length(); + var rstart = mwidth - rwidth; + ctx.save();//s8 + ctx.translate(offset * metrics.stack_width, 0); + ctx.fillStyle = "rgb(240, 240, 240)"; + if (pspm.get_left_trim() > 0) ctx.fillRect(0, 0, lwidth, metrics.stack_height); + if (pspm.get_right_trim() > 0) ctx.fillRect(rstart, 0, rwidth, metrics.stack_height); + ctx.fillStyle = "rgb(51, 51, 51)"; + if (pspm.get_left_trim() > 0) draw_dashed_line(ctx, [3], 0, lwidth-0.5, 0, lwidth-0.5, metrics.stack_height); + if (pspm.get_right_trim() > 0) draw_dashed_line(ctx, [3], 0, rstart+0.5, 0, rstart+0.5, metrics.stack_height); + ctx.restore();//s8 + }
function draw_logo_on_canvas(logo, canvas, show_names, scale) { var draw_name = (typeof show_names == "boolean" ? show_names : (logo.get_rows() > 1)); @@ -1089,6 +1177,10 @@ //translate across past the scale ctx.translate(metrics.y_label_height + metrics.y_label_spacer + metrics.y_num_width + metrics.y_tic_width, 0); + //draw the trimming background + if (pspm.get_left_trim() > 0 || pspm.get_right_trim() > 0) { + draw_trim_background(ctx, metrics, pspm, offset); + } //draw letters ctx.translate(0, metrics.y_num_height / 2); for (var col_index = 0; col_index < logo.get_columns(); col_index++) { @@ -1211,15 +1303,8 @@ element.parentNode.replaceChild(canvas, element); }
- //example code for creating a logo - //function do_load() { - // var alphabet = new Alphabet(document.getElementById("alphabet").value, document.getElementById("bgfreq").value); - // var pspm = new Pspm(document.getElementById("pspm1").value); - // var pspm_rc = pspm.copy().reverse_complement(alphabet); - // draw_logo(pspm, alphabet, "Motif 1", "logo1"); - // draw_logo(pspm_rc, alphabet, "Motif 1 Reverse Complement", "logo_rc1"); - //} - + /* END INCLUDED FILE "motif_logo.js" */ +
function setup() { var motif_count = 1; @@ -1377,15 +1462,15 @@ } </script></head> -<body onload="javascript:setup()"><form enctype="application/x-www-form-urlencoded" method="post" target="_new" action="http://dan/meme_request.cgi"> +<body onload="javascript:setup()"><form enctype="application/x-www-form-urlencoded" method="post" target="_new" action="http://straub/meme/cgi-bin/meme_request.cgi"><!--+++++++++++++++++++++++START DATA+++++++++++++++++++++++++++++++++++++--> -<input type="hidden" name="version" value="MEME version 4.5.0"> +<input type="hidden" name="version" value="MEME version 4.6.0"><input type="hidden" name="alphabet" id="alphabet" value="ACDEFGHIKLMNPQRSTVWY"><input type="hidden" name="strands" value="none"><input type="hidden" name="bgfreq" id="bgfreq" value="A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 W 0.001 Y 0.001"> -<input type="hidden" name="name" value="dan.dat"> +<input type="hidden" name="name" value="dataset_3.dat"><input type="hidden" name="combinedblock" value=" chr21_19617074_19617124_+ 1.22e-03 1 50 1 39 3.06e-05 chr21_26934381_26934431_+ 2.21e-03 1 50 1 27 5.52e-05 @@ -2179,12 +2264,12 @@ </tbody></table></div> -<p>Time 1.6 secs.</p> +<p>Time 2.1 secs.</p></div><div class="bar"><div style="text-align:right;"><a href="#top_buttons">Top</a></div><div class="subsection"> -<a name="version"></a><h5>MEME version</h5>4.5.0 (Release date: Thu Oct 14 08:44:28 EST 2010) +<a name="version"></a><h5>MEME version</h5>4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011) </div><div class="subsection"><a name="reference"></a><h5>Reference</h5> @@ -2196,7 +2281,7 @@ </div><a name="sequences"></a><a href="javascript:showHidden('trainingseq')" id="trainingseq_activator">show training set...</a><div class="subsection" id="trainingseq_data" style="display:none;"><h5>Training set:</h5> - Datafile = dan.dat<br> + Datafile = dataset_3.dat<br> Alphabet = ACDEFGHIKLMNPQRSTVWY<br><table><col><col> @@ -2387,19 +2472,19 @@ </div><a href="javascript:hideShown('trainingseq')" style="display:none;" id="trainingseq_deactivator">hide training set...</a><div class="subsection"><a name="command"></a><h5>Command line summary</h5> -<textarea rows="1" style="width:100%;" readonly>meme dan.dat -o /dataset_dan_files -nostatus </textarea><br> +<textarea rows="1" style="width:100%;" readonly>meme dataset_3.dat -o dataset_4_files -nostatus </textarea><br> Letter frequencies in dataset<br><div style="margin-left:25px;">A: 0.294 C: 0.231 D: 0.000 E: 0.000 F: 0.000 G: 0.257 H: 0.000 I: 0.000 K: 0.000 L: 0.000 M: 0.000 N: 0.000 P: 0.000 Q: 0.000 R: 0.000 S: 0.000 T: 0.217 V: 0.000 W: 0.000 Y: 0.000</div><br> Background letter frequencies (from dataset with add-one prior applied):<br><div style="margin-left:25px;">A: 0.291 C: 0.229 D: 0.001 E: 0.001 F: 0.001 G: 0.255 H: 0.001 I: 0.001 K: 0.001 L: 0.001 M: 0.001 N: 0.001 P: 0.001 Q: 0.001 R: 0.001 S: 0.001 T: 0.215 V: 0.001 W: 0.001 Y: 0.001</div><br></div><div class="subsection"> -<a name="stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs = 1 reached. Program ran on <i>dan</i>. +<a name="stopped"></a><h5>Stopping Reason</h5>Stopped because nmotifs = 1 reached. Program ran on <i>scofield</i>. </div><a href="javascript:showHidden('model')" id="model_activator">show model parameters...</a><div class="subsection" id="model_data" style="display:none;"><h5>Model parameters</h5><textarea style="width:100%;" rows="28" readonly> -host = dan +host = scofield type = zoops nmotifs = 1 evalue_threshold = inf
--- a/test-data/meme/meme/meme_output_txt_1.txt Fri Feb 25 13:35:27 2011 -0500 +++ b/test-data/meme/meme/meme_output_txt_1.txt Fri Feb 25 14:58:35 2011 -0500 @@ -1,7 +1,7 @@ ******************************************************************************** MEME - Motif discovery tool ******************************************************************************** -MEME version 4.5.0 (Release date: Thu Oct 14 08:44:28 EST 2010) +MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011)
For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. @@ -28,7 +28,7 @@ ******************************************************************************** TRAINING SET ******************************************************************************** -DATAFILE= dan.dat +DATAFILE= dataset_3.dat ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ @@ -55,7 +55,7 @@ This information can also be useful in the event you wish to report a problem with the MEME software.
-command: meme dan.dat -o dan/dataset_dan_files -nostatus +command: meme dataset_3.dat -o dataset_4_files -nostatus
model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values @@ -267,7 +267,7 @@
-Time 1.56 secs. +Time 2.13 secs.
********************************************************************************
@@ -320,6 +320,6 @@ Stopped because nmotifs = 1 reached. ********************************************************************************
-CPU: dan +CPU: scofield
********************************************************************************
--- a/test-data/meme/meme/meme_output_xml_1.xml Fri Feb 25 13:35:27 2011 -0500 +++ b/test-data/meme/meme/meme_output_xml_1.xml Fri Feb 25 14:58:35 2011 -0500 @@ -157,8 +157,8 @@
]><!-- Begin document body --> -<MEME version="4.5.0" release="Thu Oct 14 08:44:28 EST 2010"> -<training_set datafile="/dan_110.dat" length="30"> +<MEME version="4.6.0" release="Thu Jan 20 14:06:48 PST 2011"> +<training_set datafile="dataset_3.dat" length="30"><alphabet id="amino-acid" length="20"><letter id="letter_A" symbol="A"/><letter id="letter_C" symbol="C"/> @@ -183,6 +183,8 @@ </alphabet><ambigs><letter id="letter_B" symbol="B"/> +<letter id="letter_J" symbol="J"/> +<letter id="letter_O" symbol="O"/><letter id="letter_U" symbol="U"/><letter id="letter_X" symbol="X"/><letter id="letter_Z" symbol="Z"/> @@ -245,8 +247,8 @@ </letter_frequencies></training_set><model> -<command_line>meme /dan.dat -o /dataset_dan_files -nostatus </command_line> -<host>dan</host> +<command_line>meme dataset_3.dat -o dataset_4_files -nostatus </command_line> +<host>scofield</host><type>zoops</type><nmotifs>1</nmotifs><evalue_threshold>inf</evalue_threshold> @@ -300,7 +302,7 @@ </background_frequencies></model><motifs> -<motif id="motif_1" name="1" width="11" sites="25" ic="40.0" re="13.8" llr="239" e_value="2.4e-011" bayes_threshold="5.33554" elapsed_time="1.563760"> +<motif id="motif_1" name="1" width="11" sites="25" ic="40.0" re="13.8" llr="239" e_value="2.4e-011" bayes_threshold="5.33554" elapsed_time="2.128133"><scores><alphabet_matrix><alphabet_array>
--- a/tools/meme/meme.xml Fri Feb 25 13:35:27 2011 -0500 +++ b/tools/meme/meme.xml Fri Feb 25 14:58:35 2011 -0500 @@ -319,7 +319,7 @@ <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/><param name="options_type_selector" value="basic"/><param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="14"/> + <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/><output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/><output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/></test>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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