Navigation

Changeset 266

Timestamp:

01/19/08 01:09:31 (10 months ago)

Author:

Message:

added simple motif search of a sequence

Files:

r265	r266
5	5	mymembers = ('motif', 'mismatches')
6	6
	7	def search(self, sequence):
	8	"""
	9	sequence is FolderSequence.
	10	"""
	11	import motility
	12
	13	return motility.find_iupac(sequence.seq, self.motif, self.mismatches)
	14
7	15	def extra_information(self):
8	16	return "motif: %s; match %d/%d by default" % \

r265	r266
5	5	mymembers = ('name', 'motif_type', 'folder_id', 'visible')
6	6
	7	def search(self, sequence):
	8	raise NotImplementedError
	9
7	10	def extra_information(self):
8	11	raise NotImplementedError

r265	r266
4	4
5	5	import cartwheel.website
	6	from canal.motif.analyze import AnalyzeSequenceHandler
6	7	from pages import add_iupac, _q_index
7	8
8		_q_exports = ['add_iupac', 'delete', 'edit']
	9	_q_exports = ['add_iupac', 'delete', 'edit', 'go_analyze' ]
9	10
10	11	def edit(request):
11		~~pass~~
	12	assert 0
12	13
13	14	def delete(request):
	15	"""
	16	Hide the given motif, identified by 'motif_id'.
	17	"""
14	18	manager = cartwheel.website.get_object_manager()
15	19
…	…
20	24
21	25	return request.redirect(request.get_url(1))
	26
	27	def go_analyze(request):
	28	"""
	29	Redirect to the sequence analysis handler.
	30	"""
	31	seq_id = request.form['seq']
	32	return request.redirect('./analyze%s' % (seq_id,))
	33
	34	def _q_lookup(request, component):
	35	if component.startswith('analyze'):
	36	sequence_id = int(component[len('analyze'):])
	37
	38	m = cartwheel.website.get_object_manager()
	39	sequence = m.load(sequence_id)
	40
	41	return AnalyzeSequenceHandler(sequence)

r265	r266
2	2	from canal.templates import header, footer
3	3	from cartwheel.website.IUPACMotif import IUPACMotif
	4	from canal.group.utils import make_sequence_list_widget
4	5
5	6	from quixote.form import widget
…	…
14	15	folder = manager.load(folder_id)
15	16	motifs = folder.get_motifs()
	17
	18	header("Manage motifs: motif library for folder '%s'" % (folder.name,))
	19
	20	"""
	21	<h2>Motif library for folder '%s'</h2>
	22	""" % (folder.name,)
16	23
17	24	if motifs:
…	…
53	60
54	61	<A href="add_iupac">Add a simple motif</a>
	62	<p>
55	63	"""
	64
	65	###
	66	sequences = folder.get_sequences('DNA')
	67
	68	if sequences:
	69	"""
	70	<form method="POST" action="go_analyze">
	71	Analyze DNA sequence: %s <input type='submit' value='analyze'>
	72	</form>
	73	""" % (make_sequence_list_widget('seq', sequences).render(request),)
	74	else:
	75	"""
	76	(To analyze a sequence with motifs, you must first <a href='../sequences/'>enter some sequences</a>)
	77	"""
	78
	79	"""
	80	<p>
	81	<a href="../">Return to folder menu</a>
	82	"""
	83
	84	footer()
56	85
57	86	def add_iupac(request):
…	…
100	129
101	130	### create the motif & put it into the database
	131
102	132	manager = cartwheel.website.get_object_manager()
103	133