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_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 layout(node):
if node.is_leaf():
if node.name in PROTEIN_TO_DOMAINS:
seq = PROTEIN_NAME_TO_SEQ[node.name]
protDomains = PROTEIN_TO_DOMAINS[node.name]
seqFace = SeqMotifFace(seq, protDomains, scale_factor=1.3)
add_face_to_node(seqFace, node, 0, position="aligned")
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_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 layout(node):
# print node.rank
# print node.sci_name
if getattr(node, "rank", None):
if(node.rank in ['order','class','phylum','kingdom']):
rank_face = AttrFace("sci_name", fsize=7, fgcolor="indianred")
node.add_face(rank_face, column=0, position="branch-top")
if node.is_leaf():
sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
node.add_face(sciname_face, column=0, position="branch-right")
if node.is_leaf() and not node.name=='annotation':
s=str(msa[taxids.index(int(node.name))].seq)
seqFace = SeqMotifFace(s,[[0,len(s), "seq", 10, 10, None, None, None]],scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
# gi=taxid2gi[int(node.name)]
add_face_to_node(TextFace(' '+msa[taxids.index(int(node.name))].id),node,column=1, position = "aligned")
# add_face_to_node(TextFace(' '+str(int(node.name))+' '),node,column=2, position = "aligned")
# add_face_to_node(TextFace(' '+str(gi2variant[gi])+' '),node,column=3, position = "aligned")
if node.is_leaf() and node.name=='annotation':
if(annotation):
s=annotation
# get_hist_ss_in_aln_as_string(msa_tr)
else:
s=' '*len(msa[0].seq)
seqFace = SeqMotifFace(s,[[0,len(s), "seq", 10, 10, None, None, None]],scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
add_face_to_node(TextFace(' '+'SEQ_ID'),node,column=1, position = "aligned")
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(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_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_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 layout(node):
node.img_style["size"] = 0
node.img_style['hz_line_width'] = 2
node.img_style['vt_line_width'] = 2
if node.is_leaf():
# parse names
fields = node.orig_name.split("__")
name = fields[1].replace('_', ' ')
code = "%s" %fields[0].strip()
# Specie name
nF = TextFace(name, fsize=12, fgcolor='#444', fstyle='italic')
add_face_to_node(nF, node, column=0, position='aligned')
# Species code
cF = TextFace(code, fsize=12, fgcolor='grey')
cF.margin_left = 4
cF.margin_right = 4
add_face_to_node(cF, node, column=1, position='branch-right')
# Lead node styling
node.img_style['hz_line_color'] = "green"
node.img_style['vt_line_color'] = "green"
else:
# L90: green, L70: blue, L50: dark blue, L30: pink and L10: red. For the species
# tree discordance test we collapse all branches below L90.
B = float(node.B)
if B >= 90:
color = "green"
elif B >= 70:
color = "blue"
elif B >= 50:
color = "darkblue"
elif B >= 30:
color = "pink"
elif B >= 10:
color = "red"
else:
color = "yellow"
node.img_style['hz_line_color'] = color
node.img_style['vt_line_color'] = color
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 layout(node):
# print node.rank
# print node.sci_name
if getattr(node, "rank", None):
if (node.rank in ['order', 'class', 'phylum', 'kingdom']):
rank_face = AttrFace("sci_name", fsize=7, fgcolor="indianred")
node.add_face(rank_face, column=0, position="branch-top")
if node.is_leaf():
sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
node.add_face(sciname_face, column=0, position="branch-right")
if node.is_leaf() and not node.name == 'annotation':
s = str(msa[taxids.index(int(node.name))].seq)
seqFace = SeqMotifFace(
s, [[0, len(s), "seq", 10, 10, None, None, None]],
scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
# gi=taxid2gi[int(node.name)]
add_face_to_node(TextFace(' ' +
msa[taxids.index(int(node.name))].id),
node,
column=1,
position="aligned")
# add_face_to_node(TextFace(' '+str(int(node.name))+' '),node,column=2, position = "aligned")
# add_face_to_node(TextFace(' '+str(gi2variant[gi])+' '),node,column=3, position = "aligned")
if node.is_leaf() and node.name == 'annotation':
if (annotation):
s = annotation
# get_hist_ss_in_aln_as_string(msa_tr)
else:
s = ' ' * len(msa[0].seq)
seqFace = SeqMotifFace(
s, [[0, len(s), "seq", 10, 10, None, None, None]],
scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
add_face_to_node(TextFace(' ' + 'SEQ_ID'),
node,
column=1,
position="aligned")
def layout(node):
# print node.rank
# print node.sci_name
if getattr(node, "rank", None):
if(node.rank in ['order','class','phylum','kingdom']):
rank_face = AttrFace("sci_name", fsize=7, fgcolor="indianred")
node.add_face(rank_face, column=0, position="branch-top")
if node.is_leaf():
sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
node.add_face(sciname_face, column=0, position="branch-right")
if node.is_leaf() and not node.name=='annotation':
#here we are adding faces and we need to play with seqmotif face
seq=str(seqreclist[taxids.index(int(node.name))].seq)
motifs=[]#[[0,len(seq), "seq", 10, 10, None, None, None]]
for f in seqreclist[taxids.index(int(node.name))].features:
if f.type=='domain':
motifs.append([f.location.start,f.location.end,"[]",None,10,"blue", get_color(f.qualifiers['name']), "arial|8|black|%s"%f.qualifiers['name']])
if f.type=='motif':
#It turns out that we need to solve overlap problem here, here it is solved only in case of one overlap
s=f.location.start
e=f.location.end
flag=True
overlappedm=[]
for m in motifs:
if m[2]=='seq' and m[0]<e and m[1]>s: #we have an overlap, four cases, preceding motife always is on top
flag=False
overlappedm.append(m)
if not flag: #we have to solve multiple overlap problem
#let's do it by scanning
sflag=False
eflag=False
for x in range(s,e+1):
if not sflag: #check if we can start
overlap=False
for m in overlappedm:
if x>=m[0] and x<m[1]:
overlap=True
if not overlap:
ts=x
sflag=True
#check if is time to end
if sflag and not eflag:
overlap=False
for m in overlappedm:
if x==m[0]:
overlap=True
if overlap or x==e:
te=x
eflag=True
if sflag and eflag:
motifs.append([ts,te,"seq",10,10,"black",get_color(f.qualifiers['name']),None])
sflag=False
eflag=False
if flag:
motifs.append([f.location.start,f.location.end,"seq",10,10,"black",get_color(f.qualifiers['name']),None])
seqFace = SeqMotifFace(seq,motifs,scale_factor=1,seq_format="[]")
seqFace.overlaping_motif_opacity = 1.0
# seqFace.fg=aafgcolors
# seqFace.bg=aabgcolors_gray
add_face_to_node(seqFace, node, 0, position="aligned")
# gi=taxid2gi[int(node.name)]
add_face_to_node(TextFace(' '+seqreclist[taxids.index(int(node.name))].id+' '),node,column=1, position = "aligned")
# add_face_to_node(TextFace(' '+str(int(node.name))+' '),node,column=2, position = "aligned")
# add_face_to_node(TextFace(' '+str(gi2variant[gi])+' '),node,column=3, position = "aligned")
#We currently disable annotation
if node.is_leaf() and node.name=='annotation':
if(annotation):
s=annotation
# get_hist_ss_in_aln_as_string(msa_tr)
else:
s=' '*max(map(lambda x: len(x.seq),seqreclist))
def layout(node):
# print node.rank
# print node.sci_name
if getattr(node, "rank", None):
if (node.rank in ['order', 'class', 'phylum', 'kingdom']):
rank_face = AttrFace("sci_name", fsize=7, fgcolor="indianred")
node.add_face(rank_face, column=0, position="branch-top")
if node.is_leaf():
sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
node.add_face(sciname_face, column=0, position="branch-right")
if node.is_leaf() and not node.name == 'annotation':
#here we are adding faces and we need to play with seqmotif face
seq = str(seqreclist[taxids.index(int(node.name))].seq)
motifs = [] #[[0,len(seq), "seq", 10, 10, None, None, None]]
for f in seqreclist[taxids.index(int(node.name))].features:
if f.type == 'domain':
motifs.append([
f.location.start, f.location.end, "[]", None, 10,
"blue",
get_color(f.qualifiers['name']),
"arial|8|black|%s" % f.qualifiers['name']
])
if f.type == 'motif':
#It turns out that we need to solve overlap problem here, here it is solved only in case of one overlap
s = f.location.start
e = f.location.end
flag = True
overlappedm = []
for m in motifs:
if m[2] == 'seq' and m[0] < e and m[
1] > s: #we have an overlap, four cases, preceding motife always is on top
flag = False
overlappedm.append(m)
if not flag: #we have to solve multiple overlap problem
#let's do it by scanning
sflag = False
eflag = False
for x in range(s, e + 1):
if not sflag: #check if we can start
overlap = False
for m in overlappedm:
if x >= m[0] and x < m[1]:
overlap = True
if not overlap:
ts = x
sflag = True
#check if is time to end
if sflag and not eflag:
overlap = False
for m in overlappedm:
if x == m[0]:
overlap = True
if overlap or x == e:
te = x
eflag = True
if sflag and eflag:
motifs.append([
ts, te, "seq", 10, 10, "black",
get_color(f.qualifiers['name']), None
])
sflag = False
eflag = False
if flag:
motifs.append([
f.location.start, f.location.end, "seq", 10, 10,
"black",
get_color(f.qualifiers['name']), None
])
seqFace = SeqMotifFace(seq,
motifs,
scale_factor=1,
seq_format="[]")
seqFace.overlaping_motif_opacity = 1.0
# seqFace.fg=aafgcolors
# seqFace.bg=aabgcolors_gray
add_face_to_node(seqFace, node, 0, position="aligned")
# gi=taxid2gi[int(node.name)]
add_face_to_node(
TextFace(' ' + seqreclist[taxids.index(int(node.name))].id +
' '),
node,
column=1,
position="aligned")
# add_face_to_node(TextFace(' '+str(int(node.name))+' '),node,column=2, position = "aligned")
# add_face_to_node(TextFace(' '+str(gi2variant[gi])+' '),node,column=3, position = "aligned")
#We currently disable annotation
if node.is_leaf() and node.name == 'annotation':
if (annotation):
s = annotation
# get_hist_ss_in_aln_as_string(msa_tr)
else:
s = ' ' * max(map(lambda x: len(x.seq), seqreclist))
def layout(node):
if node.is_leaf():
seqFace = SeqMotifFace(seq, motifs, scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
def my_layout(node): F = TextFace(node.name, tight_text=True) add_face_to_node(F, node, column=0, position="branch-right")
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_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 layout(node):
node.img_style["size"] = 0
node_name = node.name.replace(".bam", "")
if node.is_leaf():
col_country = header2column[sample_info["country"].get(node_name, "")]
col_city = header2column[sample_info["city"].get(node_name, "")]
ssize = 40
countryF = RectFace(120, ssize, column_color[col_country],
column_color[col_country])
cityF = RectFace(120, ssize, column_color[col_city],
column_color[col_city])
if node_name in OBESITY:
if OBESITY[node_name] == "obese":
ocolor = "red"
else:
ocolor = "black"
add_face_to_node(TextFace(OBESITY[node_name],
fsize=18,
fgcolor=ocolor),
node,
header2column["obesity"],
position="aligned")
if node_name in DIABETES:
ocolor = "purple"
add_face_to_node(TextFace(DIABETES[node_name],
fsize=18,
fgcolor=ocolor),
node,
header2column["diabetes"],
position="aligned")
add_face_to_node(countryF, node, col_country, position="aligned")
add_face_to_node(cityF, node, col_city, position="aligned")
add_face_to_node(TextFace("%s" % (node.name[:25]), fsize=20),
node,
0,
position='branch-right')
else:
if args.collapse_identical and len(node.children) > 50:
node.img_style["draw_descendants"] = False
node.img_style["size"] = 20
node.img_style["shape"] = "square"
node.img_style["hz_line_width"] = 5
node.dist = 0.0001
add_face_to_node(TextFace("%d samples without data" %
len(node.children),
fsize=20),
node,
0,
position='branch-right')
