def json(self):
"""
Return coordinates for blobs in JSON format.
"""
picture_class = pygr_draw.PythonList
pic = pygr_draw.draw_annotation_maps(self.interval,
self.nlmsa_list,
picture_class=picture_class,
wrappers=self.wrappers)
l = pic.finalize()
return json.dumps(l)
def png(self):
"""
Draw & return a png for the given interval / NLMSAs.
"""
from pygr_draw.BitmapSequencePicture import BitmapSequencePicture
picture_class = BitmapSequencePicture
pic = pygr_draw.draw_annotation_maps(self.interval,
self.nlmsa_list,
picture_class=picture_class,
wrappers=self.wrappers)
image = pic.finalize()
response = quixote.get_response()
response.set_content_type('image/png')
return image
from pygr import seqdb
genome = seqdb.BlastDB('example.fa')
sequence_name = 'chrI'
import pygr_draw
from pygr_draw import AnnotationGroup, Annotation
picture_class = pygr_draw.BitmapSequencePicture
colors = picture_class.colors
annotations2 = {}
annotations2['blip'] = Annotation('blip', sequence_name, 25, 75, color=colors.green)
annotations2['gene1'] = AnnotationGroup('gene1', sequence_name, ((50, 100), (200, 300), (500, 1500)),color=colors.red)
annotations2['gene2'] = AnnotationGroup('gene2', sequence_name, ((100, 300), (1500, 2000), (3000, 3750)),color=colors.blue)
annotations2['gene3'] = AnnotationGroup('gene3', sequence_name, ((3800, 4000), (
4500, 5000)),color=colors.blue)
annotations_map = pygr_draw.create_annotation_map(annotations2, genome)
p = pygr_draw.draw_annotation_maps(genome[sequence_name][:4000],(annotations_map,),picture_class=picture_class)
image = p.finalize()
filename = 'group-example.png'
open(filename, 'w').write(image)
print 'Output in', filename
def json(self):
"""
Return coordinates for blobs in JSON format.
"""
#use request.form instead??
request = quixote.get_request().get_fields()
#request should contain:
# rel: relation - "view", "left", "right", "zin", "zout"
# sequence
# start
# stop
try:
start=int(request['start'])
stop=int(request['stop'])
sequence=request['sequence']
except KeyError:
assert False, "Incomplete AJAX request."
# we may want to raise a 501 server error here that the ajax can catch
assert start!=stop, "Sequence start and stop are invalid."
#Calculate the old interval
interval = '%s:%d-%d' % (sequence, start, stop)
ival = parse_interval_string(self.genome_db, interval)
parent_len = len(ival.pathForward)
if request['rel']=='view':
start = max(start, 0)
stop = min(stop, parent_len)
elif request['rel']=='left':
start = max(ival.start - len(ival)/2, 0)
stop = min(start + len(ival), parent_len)
elif request['rel']=='zin':
start = ival.start + len(ival) / 4
stop = ival.stop - len(ival) / 4
elif request['rel']=='zout':
start = max(ival.start - len(ival)/2, 0)
stop = min(ival.stop + len(ival)/2, parent_len)
elif request['rel']=='right':
start = max(ival.start + len(ival)/2, 0)
stop = min(start + len(ival), parent_len)
#Calculate the new interval
interval = '%s:%d-%d' % (request['sequence'], start, stop)
ival = parse_interval_string(self.genome_db, interval)
#get the data for the canvas drawing
jsonObj=""
if(USE_PYTHONLIST):
from pygr_draw.PythonList import PythonList
picture_class = PythonList
pic = pygr_draw.draw_annotation_maps(ival,
self.nlmsa_list,
picture_class=picture_class,
wrappers=self.wrappers)
jsonObj = pic.finalize()
return json.dumps({"start":start,"stop":stop,"sequence":sequence,"data":jsonObj})
else:
from pygr_draw.JSONSequencePicture import JSONSequencePicture
picture_class = JSONSequencePicture
pic = pygr_draw.draw_annotation_maps(ival,
self.nlmsa_list,
picture_class=picture_class,
wrappers=self.wrappers)
jsonObj = pic.finalize()
return json.dumps({"start":start,"stop":stop,"sequence":sequence,"data":jsonObj})
est_map = '/u/t/dev/lamprey-est-map/data/52/aln-52'
al1 = cnestedlist.NLMSA(est_map)
# plot the ESTs with names == sequence.id, color == 'red'
wrapper_est = SequenceWrapperFactory(color='red')
reads_filename = '/u/t/dev/lamprey-est-map/data/brain-rnaseq/lamprey30M2H/s_1_al-trim3-20'
al2 = cnestedlist.NLMSA(reads_filename)
wrapper_read = SequenceWrapperFactory(name='')
# because we're not using pygr.Data, the NLMSAs have different seqdbs
# for the supercontigs. We have to munge them to make them the same
# so that we can do a single draw. EVIL. Ignore Me.
sc = al1.seqDict.prefixDict['supercontigs']
al2.seqDict.prefixDict['supercontigs'] = al1.seqDict.prefixDict['supercontigs']
al2.seqDict.dicts[sc] = 'supercontigs'
# choose the sequence to plot
contig1 = al1.seqDict['supercontigs.Contig0'][:5000]
# build a png
picture_class = pygr_draw.BitmapSequencePicture
p = pygr_draw.draw_annotation_maps(contig1, (al1, al2),
picture_class=picture_class,
wrappers=(wrapper_est, wrapper_read))
# write out
image = p.finalize()
filename = 'draw.png'
open(filename, 'w').write(image)