7:58 p.m.
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>
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