def blast_closest(fasta, e=1e-10):
f = NCBIWWW.qblast("blastn", "nr", fasta, expect=e, hitlist_size=1)
rec = NCBIXML.read(f)
d = rec.descriptions[0]
result = Storage()
gi = re.findall(r'gi[|]([0-9]+)', d.title) or None
if gi: result.gi = int(gi[0])
ac = re.findall(r'gb[|]([^|]+)', d.title) or None
if ac: result.ac = ac[0].split(".")[0]
result.title = d.title.split("|")[-1].strip()
return result
def blast_closest(fasta, e=1e-10):
f = NCBIWWW.qblast("blastn", "nr", fasta, expect=e, hitlist_size=1)
rec = NCBIXML.read(f)
d = rec.descriptions[0]
result = Storage()
gi = re.findall(r'gi[|]([0-9]+)', d.title) or None
if gi: result.gi = int(gi[0])
ac = re.findall(r'gb[|]([^|]+)', d.title) or None
if ac: result.ac = ac[0].split(".")[0]
result.title = d.title.split("|")[-1].strip()
return result
def render_node_label(node, isleaf, onclick=None):
if not onclick: onclick = lambda x: ""
node_id = node.rec.id
if isleaf and node.rec.otu.taxon:
label = node.rec.otu.taxon.name
else:
label = node.label or ""
style = Storage()
if isleaf:
anchor = A(label, _onclick=onclick(node_id))
d = SPAN(anchor, _style="cursor:pointer;")
else:
anchor = A(label, _onclick=onclick(node_id))
d = SPAN(anchor, _style="background-color:yellow;cursor:pointer;")
return d
def search_namebank(term, keycode=KEY):
assert keycode, "set parameter 'keycode' or os.environ['UBIOKEY']"
params = dict(function="namebank_search",
searchName=term,
sci=1,
keyCode=keycode)
url = (WSURL + "?" + "&".join("%s=%s" % (k, v) for k, v in params.items()))
e = etree.parse(url)
v = []
for rec in e.findall("scientificNames/value"):
d = Storage()
for c in rec.iterchildren():
s = c.text
if c.tag in ("nameString", "fullNameString"):
s = b64decode(s)
d[c.tag] = s
v.append(d)
return v
def __init__(self, fig, rect, *args, **kwargs):
self.app = kwargs.pop("app", None)
self.support = kwargs.pop("support", 70.0)
self.snap = kwargs.pop("snap", True)
self.scaled = kwargs.pop("scaled", True)
self.leaflabels = kwargs.pop("leaflabels", True)
self.branchlabels = kwargs.pop("branchlabels", True)
self._mark_named = kwargs.pop("mark_named", True)
self.name = None
Axes.__init__(self, fig, rect, *args, **kwargs)
self.nleaves = 0
self.callbacks.connect("ylim_changed", self.draw_labels)
self.highlighted = None
self.highlightpatch = None
self.pan_start = None
self.decorators = {
"__selected_nodes__": (Tree.highlight_selected_nodes, [], {})
}
self.decorations = Storage()
self._active = False
self.selector = RectangleSelector(self, self.rectselect, useblit=True)
def f(e):
if e.button != 1: return True
else: return RectangleSelector.ignore(self.selector, e)
self.selector.ignore = f
self.xoffset_value = 0.05
self.selected_nodes = set()
self.leaf_offset = 4
self.leaf_valign = "center"
self.leaf_halign = "left"
self.leaf_fontsize = 10
self.branch_offset = -5
self.branch_valign = "center"
self.branch_halign = "right"
self.branch_fontsize = 10
self.spines["top"].set_visible(False)
self.spines["left"].set_visible(False)
self.spines["right"].set_visible(False)
self.xaxis.set_ticks_position("bottom")
def style_nodes(root, collapsed=None, selected_node_id=None, wscale=1.0):
style = defaultdict(Storage)
collapsed = collapsed or set()
bgcolor = "gray"
selcolor = "red"
leaves = getleaves(root, collapsed=collapsed)
l2d = leaf_distances(root, collapsed=collapsed)
height = len(leaves) * 2.5
unit = 3.0
width = max([l2d[lf] for lf in leaves]) * unit * wscale
width = min(width, 65)
rpad = max([len(lf.label or "") for lf in leaves]) * 0.7
lpad = max(1, len(root.label or []) * 0.7)
width += rpad + 2 + lpad
branchwidth = 0.75
n2c = layout.calc_node_positions(root,
width,
height,
lpad=lpad + 1,
tpad=1,
bpad=2.5,
rpad=rpad + 1,
collapsed=collapsed,
scaled=False)
n2c[root].px = 1
for node in root.iternodes(f=lambda x: x.rec.id not in collapsed):
coords = n2c[node]
style[node].x = coords.x
style[node].y = coords.y
w = coords.x - coords.px
pos = "absolute"
style[node].hbranch = Storage()
hbranch = style[node].hbranch
hbranch["position"] = pos
hbranch["width"] = w
hbranch["height"] = branchwidth
hbranch["top"] = coords.y + 0.5
hbranch["left"] = coords.px
hbranch["background-color"] = bgcolor
if float(node.rec.bootstrap_support or 0) > 0.70:
hbranch["background-color"] = "green"
if coords.py is None:
coords.py = coords.y
if coords.py < coords.y:
h = coords.y - coords.py
y = coords.py
else:
h = coords.py - coords.y
y = coords.y
style[node].vbranch = Storage()
vbranch = style[node].vbranch
vbranch["position"] = pos
vbranch["width"] = 0.5 * branchwidth
vbranch["height"] = h
vbranch["top"] = y + 0.5
vbranch["left"] = coords.px
vbranch["background-color"] = bgcolor
style[node].label = Storage()
label = style[node].label
label["position"] = pos
if node.isleaf or node.rec.id in collapsed:
label["top"] = coords.y - 0.75
label["left"] = coords.x + 0.25
if node.rec.otu and node.rec.otu.taxon:
s = node.rec.otu.taxon.name
label["width"] = len(s)
else:
label["width"] = len(node.label or "")
label["text-align"] = "left"
else:
label["text-align"] = "right"
label["width"] = len(node.label or "")
label["top"] = coords.y - 0.75
label["left"] = coords.x - len(str(node.label or ""))
style[node].ref = Storage()
ref = style[node].ref
ref["position"] = pos
ref["top"] = coords.y - 0.5
ref["left"] = coords.x + 0.25
if selected_node_id:
for n in root.iternodes(f=lambda x: x.rec.id not in collapsed):
if n.rec.id == selected_node_id:
for m in n.iternodes():
style[m].vbranch["background-color"] = selcolor
style[m].hbranch["background-color"] = selcolor
break
return width, height, style