Пример #1
0
Файл: view.py Проект: ctb/willow
 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)
Пример #2
0
Файл: view.py Проект: ctb/willow
 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
Пример #3
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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
Пример #4
0
    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})
Пример #5
0
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)