def printer_prune_taxa():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
except:
session.flash = "no tree '%s'" % i
redirect("index")
v = request.vars.nodeselect
if v:
nodes = [n for n in t.root.iternodes() if str(n.id) in v]
## for n in nodes:
while nodes:
n = nodes[0]
if n.parent:
p = n.parent
p.children.remove(n)
if p.parent and len(p.children) == 1:
gp = p.parent
c = p.children[0]
if p.length:
c.length += p.length
c.parent = gp
gp.children.insert(gp.children.index(p), c)
gp.children.remove(p)
nodes = [n for n in t.root.iternodes() if str(n.id) in v]
t.newick = newick.tostring(t.root) + ";"
t.count_nodes()
redirect(URL(r=request, f="printer", vars=dict(i=i)))
def printer_prune_taxa():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
except:
session.flash = "no tree '%s'" % i
redirect("index")
v = request.vars.nodeselect
if v:
nodes = [n for n in t.root.iternodes() if str(n.id) in v]
## for n in nodes:
while nodes:
n = nodes[0]
if n.parent:
p = n.parent
p.children.remove(n)
if p.parent and len(p.children) == 1:
gp = p.parent
c = p.children[0]
if p.length:
c.length += p.length
c.parent = gp
gp.children.insert(gp.children.index(p), c)
gp.children.remove(p)
nodes = [n for n in t.root.iternodes() if str(n.id) in v]
t.newick = newick.tostring(t.root) + ";"
t.count_nodes()
redirect(URL(r=request, f="printer", vars=dict(i=i)))
def parse(self, s=None):
if s:
self.newick = s
self.root = newick.parse(self.newick)
scaled = True
for i, n in enumerate(self.root.iternodes(phylo.POSTORDER)):
n.number = i
if (not n.istip) and (not n.label):
n.label = "N%s" % n.number
n.age = None
if n.parent and (n.length is None):
scaled = False
self.newick = newick.tostring(self.root)+";"
self.scaled = scaled
def printer_reroot():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
except:
session.flash = "no tree '%s'" % i
redirect("index")
v = request.vars.nodeselect
if v:
nodes = [n for n in t.root.iternodes() if str(n.id) in v]
newroot = t.root.mrca([n.label for n in nodes])
if newroot:
newroot = phylo.reroot(t.root, newroot)
t.newick = newick.tostring(newroot) + ";"
t.parse()
redirect(URL(r=request, f="printer", vars=dict(i=i)))
def printer_reroot():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
except:
session.flash = "no tree '%s'" % i
redirect("index")
v = request.vars.nodeselect
if v:
nodes = [n for n in t.root.iternodes() if str(n.id) in v]
newroot = t.root.mrca([n.label for n in nodes])
if newroot:
newroot = phylo.reroot(t.root, newroot)
t.newick = newick.tostring(newroot) + ";"
t.parse()
redirect(URL(r=request, f="printer", vars=dict(i=i)))
def printer():
tlist = get_treelist()
try:
i = int(request.vars.i)
except TypeError:
redirect("index")
try:
t = tlist.trees[i]
except IndexError:
session.flash = "no tree '%s'" % i
redirect("index")
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True,
reverse=bool(request.vars.rev))
t.newick = newick.tostring(t.root) + ";"
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
#print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = StringIO()
npages, scalefact = drawtree.render_multipage(d, opts, buf)
f = open("/tmp/%s.pdf" % fname, "w")
f.write(buf.getvalue())
f.close()
# use graphicsmagick convert (page numbers *.png.0, *.png.1, ...)
commands.getoutput("rm /tmp/%s*.png*" % fname)
cmd = "convert /tmp/%s.pdf /tmp/%s.png" % (fname, fname)
exit, out = commands.getstatusoutput(cmd)
# pngs = glob.glob("/tmp/%s*.png*" % fname)
if npages > 1:
pngs = ['%s.png.%s' % (fname, i) for i in range(npages)]
else:
pngs = ['%s.png' % fname]
if scalefact < 1.0:
response.flash = "To fit the page width, "\
"the drawing has been scaled by %0.2f" % scalefact
return dict(tree=t, pngs=pngs)
def printer():
tlist = get_treelist()
try:
i = int(request.vars.i)
except TypeError:
redirect("index")
try:
t = tlist.trees[i]
except IndexError:
session.flash = "no tree '%s'" % i
redirect("index")
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True, reverse=bool(request.vars.rev))
t.newick = newick.tostring(t.root) + ";"
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
# print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = StringIO()
npages, scalefact = drawtree.render_multipage(d, opts, buf)
f = open("/tmp/%s.pdf" % fname, "w")
f.write(buf.getvalue())
f.close()
# use graphicsmagick convert (page numbers *.png.0, *.png.1, ...)
commands.getoutput("rm /tmp/%s*.png*" % fname)
cmd = "convert /tmp/%s.pdf /tmp/%s.png" % (fname, fname)
exit, out = commands.getstatusoutput(cmd)
# pngs = glob.glob("/tmp/%s*.png*" % fname)
if npages > 1:
pngs = ["%s.png.%s" % (fname, i) for i in range(npages)]
else:
pngs = ["%s.png" % fname]
if scalefact < 1.0:
response.flash = "To fit the page width, " "the drawing has been scaled by %0.2f" % scalefact
return dict(tree=t, pngs=pngs)
