def ly_condensed_alg(self, node):
if node.is_leaf():
if 'sequence' in node.features:
seqFace = SeqMotifFace(node.sequence, [],
intermotif_format="line",
seqtail_format="line", scale_factor=1)
add_face_to_node(seqFace, node, 10, aligned=True)
def ly_leaf_names(node):
if node.is_leaf():
spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
if hasattr(node, 'genename'):
geneF = TextFace(" (%s)" %node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica')
add_face_to_node(geneF, node, column=1, position='branch-right')
def ly_block_alg(node):
if node.is_leaf():
if 'sequence' in node.features:
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c+1 == len(node.sequence):
start, end = last_lt, c
motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None])
last_lt = None
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=ALG_SCALE)
add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)
def ly_tax_labels(node):
if node.is_leaf():
c = LABEL_START_COL
largest = 0
for tname in TRACKED_CLADES:
if hasattr(node, "named_lineage") and tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.margin_right = 2
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(c, len(TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
def ly_tax_labels(self, node):
if node.is_leaf():
c = self.LABEL_START_COL
node_lin = getattr(node, "named_lineage", [])
for tname in node_lin:
if tname.lower() in self.TRACKED_CLADES:
linF = self.LIN2FACE[tname.lower()]
# linF = TextFace(tname, fsize=10, fgcolor='white')
# linF.margin_left = 3
# linF.margin_right = 2
# linF.background.color = self.LIN2COLOR[tname.lower()]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(c, len(self.TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
def ly_basic(node):
if node.is_leaf():
node.img_style['size'] = 0
else:
node.img_style['size'] = 0
node.img_style['shape'] = 'square'
if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
if node.tree_seqtype == "nt":
node.img_style["bgcolor"] = "#CFE6CA"
ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica')
add_face_to_node(ntF, node, 10, position="branch-bottom")
if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
node.img_style['size'] = 4
node.img_style['fgcolor'] = "steelblue"
node.img_style['hz_line_width'] = 1
node.img_style['vt_line_width'] = 1
def ly_block_alg(self, node):
if node.is_leaf():
if 'sequence' in node.features:
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c+1 == len(node.sequence):
start, end = last_lt, c
motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None])
last_lt = None
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=1)
add_face_to_node(seqFace, node, 10, aligned=True)
def rotation_layout(node):
if node.is_leaf():
F = TextFace(node.name, tight_text=True)
F.rotation = randint(0, 360)
add_face_to_node(TextFace("third" ), node, column=8, position="branch-right")
add_face_to_node(TextFace("second" ), node, column=2, position="branch-right")
add_face_to_node(F, node, column=0, position="branch-right")
F.border.width = 1
F.inner_border.width = 1
def ly_leaf_names(self, node):
if node.is_leaf():
if node.species != 0 and self.ncbitaxa:
spF = TextFace("%s" %getattr(node, "spname", ""), fsize=8, fgcolor='#777777', ftype='Helvetica')
geneF = TextFace("(%s)" %node.name[:50], fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
add_face_to_node(geneF, node, column=1, position='branch-right')
else:
geneF = TextFace("%s" %node.name, fsize=8, fgcolor='#777777', ftype='Helvetica')
add_face_to_node(geneF, node, column=0, position='branch-right')
def layout(node):
if node.is_leaf():
seqFace = SeqMotifFace(seq, motifs, scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
def ly_supports(self, node):
if not node.is_leaf():
supFace = TextFace("%0.3g" %(node.support), fsize=7, fgcolor='indianred')
add_face_to_node(supFace, node, column=0, position='branch-top')
def ly(node):
node.img_style['vt_line_width'] = 1
node.img_style['hz_line_width'] = 1
if node.is_leaf():
add_face_to_node(TextFace(
' (%s)' % node.name.split()[0].replace("/exon2", ""),
fsize=10,
fgcolor='slategrey',
tight_text=False),
node,
1,
position='branch-right')
add_face_to_node(TextFace(node.species,
fsize=12,
fgcolor='black',
fstyle='italic',
tight_text=False),
node,
0,
position='branch-right')
c = 1
for tname in tracked_clades:
if tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(1, 20 - (c - 1)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'),
node,
c,
position='aligned')
c += 1
if draw_alg and 'sequence' in node.features:
#seqFace = SequenceFace(node.sequence,"aa",13)
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c + 1 == len(node.sequence):
start, end = last_lt, c
w = end - start
motifs.append([
start, end, "[]", w, 13, "slategrey",
"slategrey", None
])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c - 1
w = end - start
motifs.append([
start, end, "[]", w, 13, "slategrey",
"slategrey", None
])
last_lt = None
if not motifs:
print node, node.sequence
seqFace = SeqMotifFace(node.sequence,
motifs,
intermotif_format="line",
seqtail_format="line",
scale_factor=1)
add_face_to_node(seqFace, node, 20, aligned=True)
else:
if node.up:
add_face_to_node(TextFace('% 3g' % node.support,
fsize=11,
fgcolor='indianred'),
node,
0,
position='branch-top')
if hasattr(node, "support2") and node.up:
add_face_to_node(TextFace('% 3g' % float(node.support2),
fsize=11,
fgcolor='steelblue'),
node,
0,
position='branch-bottom')
node.img_style['size'] = 0
node.img_style['hz_line_color'] = 'black'
node.img_style['vt_line_color'] = 'black'
def ly_supports(node):
if not node.is_leaf() and node.up:
supFace = TextFace("%0.2g" %(node.support), fsize=7, fgcolor='indianred')
add_face_to_node(supFace, node, column=0, position='branch-top')
def ly(node):
node.img_style['vt_line_width'] = 1
node.img_style['hz_line_width'] = 1
if node.is_leaf():
add_face_to_node(TextFace(' (%s)' %node.name.split()[0].replace("/exon2", ""), fsize=10, fgcolor='slategrey', tight_text=False), node, 1, position='branch-right')
add_face_to_node(TextFace(node.species, fsize=12, fgcolor='black', fstyle='italic', tight_text=False), node, 0, position='branch-right')
c = 1
for tname in tracked_clades:
if tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(1, 20-(c-1)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
if draw_alg and 'sequence' in node.features:
#seqFace = SequenceFace(node.sequence,"aa",13)
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c+1 == len(node.sequence):
start, end = last_lt, c
w = end-start
motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
w = end-start
motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
last_lt = None
if not motifs:
print node, node.sequence
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=1)
add_face_to_node(seqFace, node, 20, aligned=True)
else:
if node.up:
add_face_to_node(TextFace('% 3g' %node.support, fsize=11, fgcolor='indianred'), node, 0, position='branch-top')
if hasattr(node, "support2") and node.up:
add_face_to_node(TextFace('% 3g' %float(node.support2), fsize=11, fgcolor='steelblue'), node, 0, position='branch-bottom')
node.img_style['size'] = 0
node.img_style['hz_line_color'] = 'black'
node.img_style['vt_line_color'] = 'black'
def layout(node):
if node.is_leaf():
seqFace = SeqMotifFace(seq, motifs, scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")