def showTreeInGrid(gid,biome,grid_level=14,taxonomic_level='sp'):
"""
Performs a selection, spatial filter and returns an image.
grid_level is the grid layer.
taxonomic_level is the taxonomic level to be shown. Options are:
sp, gns, fam, ord, cls, phy, king
"""
mesh = initMesh(grid_level)
try:
cell = mesh.objects.get(id=id)
except:
logger.error("Selected id does not exist in selected grid")
return None
gb=GriddedTaxonomy(biome,cell,generate_tree_now=True)
forest = gb.taxonomies[0].forest
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 360
forest[taxonomic_level].show(tree_style=ts)
return 'Parece que se tiene que ver algo'
def ete_tree(aln):
"""Tree showing alleles"""
from ete2 import Tree, PhyloTree, TreeStyle, NodeStyle
t = Tree('temp.dnd')
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180
ts.arc_span = 180
cutoff = 0.25
def func(node):
if node.name == 'NoName': #or not node.name in metric:
return False
#if metric[node.name]<=cutoff:
# return True
matches = filter(func, t.traverse())
print(len(matches), "nodes have distance <=%s" % cutoff)
nst1 = NodeStyle()
nst1["bgcolor"] = "Yellow"
for n in matches:
n.set_style(nst1)
nst2 = NodeStyle()
nst2["bgcolor"] = "LightGreen"
#hlanodes = [t.get_leaves_by_name(name=r)[0] for r in refalleles]
#for n in hlanodes:
# n.set_style(nst2)
t.show(tree_style=ts)
return
def showTreeInGrid(gid, biome, grid_level=14, taxonomic_level='sp'):
"""
Performs a selection, spatial filter and returns an image.
grid_level is the grid layer.
taxonomic_level is the taxonomic level to be shown. Options are:
sp, gns, fam, ord, cls, phy, king
"""
mesh = initMesh(grid_level)
try:
cell = mesh.objects.get(id=id)
except:
logger.error("Selected id does not exist in selected grid")
return None
gb = GriddedTaxonomy(biome, cell, generate_tree_now=True)
forest = gb.taxonomies[0].forest
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 360
forest[taxonomic_level].show(tree_style=ts)
return 'Parece que se tiene que ver algo'
def ETETree(seqs, ref, metric):
"""Tree showing bola alleles covered by tepitope"""
from ete2 import Tree,PhyloTree,TreeStyle,NodeStyle
aln = Genome.clustalAlignment(seqs=seqs)
t = Tree('temp.dnd')
#t.set_outgroup(t&ref)
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180
ts.arc_span = 180
cutoff=0.25
def func(node):
if node.name=='NoName' or not node.name in metric:
return False
if metric[node.name]<=cutoff:
return True
matches = filter(func, t.traverse())
print len(matches), "nodes have distance <=%s" %cutoff
nst1 = NodeStyle()
nst1["bgcolor"] = "Yellow"
for n in matches:
n.set_style(nst1)
nst2 = NodeStyle()
nst2["bgcolor"] = "LightGreen"
hlanodes = [t.get_leaves_by_name(name=r)[0] for r in refalleles]
for n in hlanodes:
n.set_style(nst2)
t.show(tree_style=ts)
return
def ETETree(seqs, ref, metric):
"""Tree showing bola alleles covered by tepitope"""
from ete2 import Tree, PhyloTree, TreeStyle, NodeStyle
aln = Genome.clustalAlignment(seqs=seqs)
t = Tree('temp.dnd')
#t.set_outgroup(t&ref)
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180
ts.arc_span = 180
cutoff = 0.25
def func(node):
if node.name == 'NoName' or not node.name in metric:
return False
if metric[node.name] <= cutoff:
return True
matches = filter(func, t.traverse())
print len(matches), "nodes have distance <=%s" % cutoff
nst1 = NodeStyle()
nst1["bgcolor"] = "Yellow"
for n in matches:
n.set_style(nst1)
nst2 = NodeStyle()
nst2["bgcolor"] = "LightGreen"
hlanodes = [t.get_leaves_by_name(name=r)[0] for r in refalleles]
for n in hlanodes:
n.set_style(nst2)
t.show(tree_style=ts)
return
def setUp(self):
tree = Tree()
root = tree.get_tree_root()
root.dist = 0
root.name = "root"
node = root.add_child(name="Left")
node.add_child(name="Alpha")
node.add_child(name="Beta")
node = root.add_child(name="Right")
node.add_child(name="Gamma")
node.add_child(name="Delta")
for desc in tree.iter_descendants():
desc.dist = 0
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = False
ts.mode = "c"
ts.arc_start = 0
ts.arc_span = 360
self.circular_style = ts
self.exampleTree = tree
self.alignment = MultipleSeqAlignment([
SeqRecord(Seq("AAG", generic_dna), id="Alpha"),
SeqRecord(Seq("AGA", generic_dna), id="Beta"),
SeqRecord(Seq("AAA", generic_dna), id="Gamma"),
SeqRecord(Seq("GGA", generic_dna), id="Delta"),
])
def build_vis(): ts = TreeStyle() ts.mode = "c" ts.arc_start = 0 # 0 degrees = 3 o'clock ts.arc_span = 360 ts.layout_fn = my_layout # Use custom layout return ts
def showTreeInGrid(request):
"""
.. showTreeInGrid:
Performs a selection, spatial filter and returns an image.
Parameters in GET variable
===========================
grid_level : int
The grid layer.
taxonomic_level : string
The taxonomic level to be shown.
Options are: sp, gns, fam, ord, cls, phy, king
Returns
=======
HTTP RESPONSE
with an image showing the tree.
See figure:
.. image::
"""
from ete2.treeview import drawer
from PyQt4 import QtCore
import ipdb
response = HttpResponse()
get = request.GET
try:
gid = int(get['gid'])
grid_level = int(get['g_l'])
taxonomic_level = get['tax_lvl']
except:
response.content='Bad request. Check GET variable definitions'
response.status_code = 500
return response
biome = Occurrence.objects.all()
mesh = initMesh(grid_level)
try:
cell = mesh.objects.get(id=gid)
except:
logger.error("Selected id does not exist in selected grid")
return None
import os.path
head_path = settings.PATH_IMAGES
filename = "%s-%s-%s.png" %(grid_level,gid,taxonomic_level)
file_ = head_path+filename
logger.info('Writing in: %s'%file_)
if not os.path.isfile(file_):
logger.info("The image doens't exist")
gb=GriddedTaxonomy(biome,cell,generate_tree_now=True)
forest = gb.taxonomies[0].forest
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 360
try:
#ipdb.set_trace()
forest[taxonomic_level].render(file_, w=100, units="mm",tree_style=ts)
#drawer.exit_gui(1, 1)
#logger.info(QtCore.QThreadPool)
del(forest[taxonomic_level])
except:
logger.error('Something went wrong with the image rendering')
#del(forest)
#ipdb.set_trace()
template = get_template('base.html')
html = template.render(Context({'gid':gid,'taxonomic_level':taxonomic_level,'grid_level':grid_level,'image_path':filename}))
response.content=(html)
#response.content=str(forest[taxonomic_level])
response.status_code = 200
return response
def showAllLevelsInTreeInGrid(request):
"""
Performs a selection, spatial filter and returns an image.
grid_level is the grid layer.
taxonomic_level is the taxonomic level to be shown. Options are:
sp, gns, fam, ord, cls, phy, king
"""
import ipdb
response = HttpResponse()
get = request.GET
try:
gid = int(get['gid'])
grid_level = int(get['g_l'])
names = int(get['names'])
if names > 0:
only_id = False
else:
only_id = True
#taxonomic_level = get['tax_lvl']
except:
response.content='Bad request. Check GET variable definitions'
response.status_code = 500
return response
biome = Occurrence.objects.all()
mesh = initMesh(grid_level)
try:
cell = mesh.objects.get(id=gid)
except:
logger.error("Selected id does not exist in selected grid")
return None
import os.path
tax_levels = ['sp','gns','fam','cls','ord','phy','kng']
tax_keys = {'sp':'1.Species','gns':'2. Genera','fam':'3. Families','ord':'4. Orders','cls':'5. Classes','phy':'6. Phyla','kng':'7. Kingdoms'}
rich_keys = { 'oc':'occurrences','sp' :'species','gns':'genera','fam':'families','cls':'classes','ord':'orders','phy':'phyla','kng':'kingdoms'}
img_paths = {}
#THIS IS VERY VERY WRONG AND I WOULD SUGGEST A REFACTORING like the use of a binary written copy in disk about the object in question (cached)
gb=GriddedTaxonomy(biome,cell,generate_tree_now=True,use_id_as_name=only_id)
taxonomy = gb.taxonomies[0]
#ipdb.set_trace()
mat_complex = taxonomy.calculateIntrinsicComplexity()
for taxonomic_level in tax_levels:
head_path = settings.PATH_IMAGES
filename = "%s-%s-%s.png" %(grid_level,gid,taxonomic_level)
file_ = head_path+filename
logger.info('Writing in: %s'%file_)
if not os.path.isfile(file_):
logger.info("The image doens't exist")
try:
if gb not in locals():
#gb=GriddedTaxonomy(biome,cell,generate_tree_now=True)
logger.info("Gridded taxonomy doesn't found")
except:
gb=GriddedTaxonomy(biome,cell,generate_tree_now=True,use_id_as_name=only_id)
forest = taxonomy.forest
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 360
ts.show_scale = False
try:
#ipdb.set_trace()
forest[taxonomic_level].render(file_,h=500, w=500, units="px",tree_style=ts)
#drawer.exit_gui(1, 1)
#logger.info(QtCore.QThreadPool)
#del(forest[taxonomic_level])
except:
logger.error('Something went wrong with the image rendering')
img_paths[taxonomic_level] = {'name': tax_keys[taxonomic_level],'path':filename,'richness':taxonomy.richness[rich_keys[taxonomic_level]]}
else:
img_paths[taxonomic_level] = {'name': tax_keys[taxonomic_level],'path':filename,'richness':taxonomy.richness[rich_keys[taxonomic_level]]}
#del(forest)
#
#dic_richness = gb.taxonomies[0].richness
det_complex = gb.taxonomies[0].vectorIntrinsic
template = get_template('base.html')
submatrices = map(lambda i : mat_complex[0:i,0:i],range(1,len(mat_complex)))
#ipdb.set_trace()
import numpy as np
tras = map(lambda mat : np.linalg.eigvals(mat),submatrices)
#ipdb.set_trace()
try:
eigenv = np.linalg.eigvals(mat_complex).tolist()
svd = np.linalg.svd(mat_complex)
except:
eigenv =[]
svd = [[],[],[]]
#ipdb.set_trace()
html = template.render(Context({'gid':gid,'taxonomic_level':taxonomic_level,'grid_level':grid_level,'image_path':sorted(img_paths.itervalues()),'complexity':mat_complex.tolist(),'vect_comp':det_complex,'eigenv':eigenv,'left_eig_vect':svd[0].tolist(),'svd':svd[1].tolist(),'right_eig_vect':svd[2].tolist()}))
response.content=(html)
#response.content=str(forest[taxonomic_level])
response.status_code = 200
return response
#!/usr/bin/python # drawunrootedcircular.py # Use ete2 to render an unrooted tree from an input Newick formatted tree file. # Render the tree as circular. # sys.argv[1] -- filename for tree file # sys.argv[2] -- filename for output .png file import sys from ete2 import Tree, TreeStyle if( len(sys.argv) != 3 ): print "Usage: python drawunrootedcircular.py <Newick_file> <Tree_png>" exit(-1) t = Tree(sys.argv[1]) c = TreeStyle() c.mode = "c" c.scale = 50 c.arc_start = -90 c.arc_span = 360 t.render(sys.argv[2], w=720, units="px", tree_style=c)
import dateutil.parser
#from models import Count,Sum,Avg
from django.contrib.gis.db.models import Extent, Union, Collect,Count,Min
from gbif.models import Specie,Genus,Family,Order,Class,Phylum,Kingdom
from mesh.models import NestedMesh
from django.contrib.gis.db.models.query import GeoQuerySet
logger = logging.getLogger('biospatial.gbif.general_test')
import biospatial.settings as settings
# Create your tests here.
from ete2 import Tree, TreeStyle
t = Tree()
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 360
from gbif.taxonomy import Taxonomy,embedTaxonomyInGrid,embedTaxonomyInNestedGrid,NestedTaxonomy
def createShapefile(taxonomy_list,name='default_name',store='out_maps'):
"""
This function creates a shapefile for a given list of Taxonomies.
Do note that the list of taxonomies is a mapping to the cells in a mesh.
"""
#Method for generating the shapefile object
from osgeo import ogr
#from shapely.geometry import Polygon
faces.add_face_to_node(f, node, 0, position="aligned")
f.border.width = 0
#f = faces.CircleFace(20, "red")
#f = faces.AttrFace("name", fsize=20)
f = faces.TextFace("NAME", fsize=10)
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
#node.img_style["bgcolor"] = random_color()
#Tree().show()
ts = TreeStyle()
ts.mode = "c"
ts.layout_fn = layout
ts.show_leaf_name = False
ts.arc_span = 340
ts.arc_start = -70
#ts.allow_face_overlap = True
#ts.show_branch_length = True
ts.draw_guiding_lines = False
ts.optimal_scale_level = "mid"
ts.extra_branch_line_color = "red"
ts.root_opening_factor = 0.50
ts.show_border = True
ts.scale = None
t = Tree()
t.populate(200, random_branches=True, branch_range=(0, 0))
t.dist = 0.0
dists = [n.dist for n in t.traverse() if n.dist != 0]
#print max(dists), min(dists)
t.write(outfile="test.nw")
#for s in [5, None]:
## Bonus ETE dendrogram plotting
# Configure output path for image
#ete_output_path="eteTree.png"
width = 600 # For other output args, see http://etetoolkit.org/docs/latest/tutorial/tutorial_drawing.html#rendering-trees-as-images
# Configure tree styles
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_scale = False
ts.scale = None
ts.mode = "c" # draw tree in circular style
ts.arc_start = 0
ts.arc_span = 360
if orientation == "top":
ts.rotation = 90
ts.branch_vertical_margin = 10 # 10 pixels between adjacent branches
# Remove the default small red spheres for each node
nstyle = NodeStyle()
nstyle["size"] = 0
for leaf in tree:
k = leaf.name
k = int(k)
leaf.name = labels[k]
# Apply node styles to nodes
import dateutil.parser
#from models import Count,Sum,Avg
from django.contrib.gis.db.models import Extent, Union, Collect, Count, Min
from gbif.models import Specie, Genus, Family, Order, Class, Phylum, Kingdom
from mesh.models import NestedMesh
from django.contrib.gis.db.models.query import GeoQuerySet
logger = logging.getLogger('biospatial.gbif.general_test')
import biospatial.settings as settings
# Create your tests here.
from ete2 import Tree, TreeStyle
t = Tree()
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 360
from gbif.taxonomy import Taxonomy, embedTaxonomyInGrid, embedTaxonomyInNestedGrid, NestedTaxonomy
def createShapefile(taxonomy_list, name='default_name', store='out_maps'):
"""
This function creates a shapefile for a given list of Taxonomies.
Do note that the list of taxonomies is a mapping to the cells in a mesh.
"""
#Method for generating the shapefile object
from osgeo import ogr
#from shapely.geometry import Polygon
# Now convert it to a shapefile with OGR
driver = ogr.GetDriverByName('Esri Shapefile')
## Bonus ETE dendrogram plotting
# Configure output path for image
#ete_output_path="eteTree.png"
width = 600 # For other output args, see http://etetoolkit.org/docs/latest/tutorial/tutorial_drawing.html#rendering-trees-as-images
# Configure tree styles
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_scale = False
ts.scale = None
ts.mode = "c" # draw tree in circular style
ts.arc_start = 0
ts.arc_span = 360
if orientation == "top":
ts.rotation = 90
ts.branch_vertical_margin = 10 # 10 pixels between adjacent branches
# Remove the default small red spheres for each node
nstyle = NodeStyle()
nstyle["size"] = 0
for leaf in tree:
k = leaf.name
k = int(k)
leaf.name = labels[k]
# Apply node styles to nodes
