Changeset 291

Timestamp:

02/01/08 00:08:14 (10 months ago)

Author:

t

Message:

added 'palindromic' flag.

Files:

• trunk/cartwheel-server/data-model/website/motifs.sql (modified) (1 diff)
• trunk/cartwheel-server/lib/cartwheel/website/PWMMotif.py (modified) (3 diffs)
• trunk/cartwheel-server/lib/cucumber/_utils.py (modified) (1 diff)
• trunk/cartwheel-server/website/canal/motif/pages_pwm.ptl (modified) (9 diffs)

trunk/cartwheel-server/data-model/website/motifs.sql

@@ -38 +38 @@
-        class_id INTEGER REFERENCES classes DEFAULT :class_id,
-        source_motifs TEXT DEFAULT '',
+        palindromic BOOLEAN DEFAULT 'f',
-        threshold FLOAT
-) INHERITS (named_motifs);

trunk/cartwheel-server/lib/cartwheel/website/PWMMotif.py

@@ -2 +2 @@
-A PWM motif created from a list of sites.
-"""
+import fasta
-from cartwheel.website.NamedMotif import NamedMotif
-
-class PWMMotif(NamedMotif):
-    table = 'pwm_motifs'
-
+, 'palindromic'
-
-    def make_pwm(self):
@@ -12 +13 @@
-
-        sites = self.source_motifs.split("\n")
+        if self.palindromic:
+            rc_sites = [ fasta.rc(site) for site in sites ]
+            sites.extend(rc_sites)
+        
-        pwm = motility.make_pwm(sites)
-        return pwm
@@ -21 +26 @@
-        import motility
-
-
-
+
-
-        return pwm.find(sequence.seq[start:stop],

trunk/cartwheel-server/lib/cucumber/_utils.py

@@ -151 +151 @@
-    elif type(value) == DateTime.DateTimeType:
-        return "'%s'" % (str(value),)
+    elif type(value) == bool:
+        if value:
+            return "'t'"
+        else:
+            return "'f'"
-    elif value is None:
-        return 'NULL'

trunk/cartwheel-server/website/canal/motif/pages_pwm.ptl

@@ -48 +48 @@
-            errors.extend(utils.validate_pwm_input(sequences, threshold))
-
+    if 'palindromic' in request.form:
+        if request.form['palindromic'] == 'yes':
+            motif.palindromic = True
+        else:
+            motif.palindromic = False
+
-    if 'notes' in request.form:
-        notes = request.form['notes']
@@ -65 +71 @@
-    
-    # fill
+    palindromic = 'no'
+    if motif.palindromic:
+        palindromic = 'yes'
+        
-    values = dict(motif_id=motif.id,
-                  name=motif.name,
-                  sequences=motif.source_motifs,
-                  threshold=round(motif.threshold, 3),
+                  palindromic=palindromic,
-                  notes=motif.notes)
-
-lity.make_pwm(sequences
+f.make_pwm(
-
-    formhtml = """\
@@ -85 +96 @@
-<p>
-Threshold: <input type='text' name='threshold' size='7'>
+<p>
+Are binding sites palindromic?
+ <select name='palindromic'>
+   <option value='no'> No
+   <option value='yes'> Yes
+ </select>
-<p>
-Notes:<br>
@@ -98 +115 @@
-""" % (motif.name,)
-
-    formhtml = htmlfill.render(formhtml, values)
-    
-    return wrap(htmlfill.render(formhtml, values),
-                display_pwm_information(pwm, sequences, threshold),
@@ -183 +198 @@
-    ###
-
-template display_pwm_from_sites(request, name, sequences, notes):
-    header("Motif '%s' created" % (name,))
-    
-    "<h2>Matrix motif '%s' created.</h2>" % (name,)
-    
-    pwm = motility.make_pwm(sequences)
-    site_scores = [ (pwm.calc_score(s),s) for s in sequences ]
-    site_scores.sort()
-    site_scores.reverse()
-
-    lowest_score = site_scores[-1][0]
-    
-    ###
-
-    display_pwm_information(pwm, sequences, lowest_score)
-
-    ### create
-
-    manager = cartwheel.website.get_object_manager()
-
-    folder_id = request.session.get_current_folder().id
-
-    m = manager.create(PWMMotif, name=name, source_motifs="\n".join(sequences),
-                       motif_type='PWM',
-                       threshold=lowest_score,
-                       notes=notes,
-                       folder_id=folder_id)
-
-    manager.commit()
-
-    """
-    <p>
-    <a href='./edit?motif_id=%d'>Edit motif information and threshold</a>
-    <p>
-    <a href='./'>Return to motif list</a>
-    """ % (m.id,)
-
-    footer()
-
-def build_pwm_from_list(request):
-    if not request.form:
@@ -250 +226 @@
-<textarea name='sequences' rows='5' cols='30'></textarea>
-<p>
+Are binding sites palindromic?
+ <select name='palindromic'>
+   <option value='no'> No
+   <option value='yes'> Yes
+ </select>
+<p>
-Notes:<br>
-<blockquote>
@@ -283 +265 @@
-        errors.extend(utils.validate_pwm_input(sequences))
-
+    
+    if request.form['palindromic'] == 'yes':
+        palindromic = True
+    else:
+        palindromic = False
+
-    if errors:
-        return error("ERROR:<p><ul><li> %s</ul>" % ("<li>".join(errors,)))
@@ -288 +276 @@
-    ### ok, validation good so far.  build the PWM & display...
-    
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-    site_scores = [ (pwm.calc_score(s),s) for s in sequences ]
-    site_scores.sort()
@@ -301 +300 @@
-
-    lowest_score = site_scores[-1][0]
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
-    display_pwm_information(pwm, sequences, lowest_score)
-
-    ### create
-
-    manager = cartwheel.website.get_object_manager()
-
-    folder_id = request.session.get_current_folder().id
-
-    m = manager.create(PWMMotif, name=name, source_motifs="\n".join(sequences),
-                       motif_type='PWM',
-                       threshold=lowest_score,
-                       notes=notes,
-                       folder_id=folder_id)
-
-    manager.commit()
-
-    """