def run(args):
if args.text_mode:
from ete2 import Tree
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = Tree(nw)
else:
t = Tree(tfile)
print t.get_ascii(show_internal=args.show_internal_names,
attributes=args.show_attributes)
return
import random
import re
import colorsys
from collections import defaultdict
from ete2 import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle,
add_face_to_node, random_color)
global FACES
if args.face:
FACES = parse_faces(args.face)
else:
FACES = []
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = True
ts.tree_width = args.tree_width
for f in FACES:
if f["value"] == "@name":
ts.show_leaf_name = False
break
if args.as_ncbi:
ts.show_leaf_name = False
FACES.extend(parse_faces(
['value:@sci_name, size:10, fstyle:italic',
'value:@taxid, color:grey, size:6, format:" - %s"',
'value:@sci_name, color:steelblue, size:7, pos:b-top, nodetype:internal',
'value:@rank, color:indianred, size:6, pos:b-bottom, nodetype:internal',
]))
if args.alg:
FACES.extend(parse_faces(
['value:@sequence, size:10, pos:aligned, ftype:%s' %args.alg_type]
))
if args.heatmap:
FACES.extend(parse_faces(
['value:@name, size:10, pos:aligned, ftype:heatmap']
))
if args.bubbles:
for bubble in args.bubbles:
FACES.extend(parse_faces(
['value:@%s, pos:float, ftype:bubble, opacity:0.4' %bubble,
]))
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
ts.layout_fn = lambda x: None
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = PhyloTree(nw)
else:
t = PhyloTree(tfile)
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
if args.heatmap:
DEFAULT_COLOR_SATURATION = 0.3
BASE_LIGHTNESS = 0.7
def gradient_color(value, max_value, saturation=0.5, hue=0.1):
def rgb2hex(rgb):
return '#%02x%02x%02x' % rgb
def hls2hex(h, l, s):
return rgb2hex( tuple(map(lambda x: int(x*255), colorsys.hls_to_rgb(h, l, s))))
lightness = 1 - (value * BASE_LIGHTNESS) / max_value
return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)
heatmap_data = {}
max_value, min_value = None, None
for line in open(args.heatmap):
if line.startswith('#COLNAMES'):
pass
elif line.startswith('#') or not line.strip():
pass
else:
fields = line.split('\t')
name = fields[0].strip()
values = map(lambda x: float(x) if x else None, fields[1:])
maxv = max(values)
minv = min(values)
if max_value is None or maxv > max_value:
max_value = maxv
if min_value is None or minv < min_value:
min_value = minv
heatmap_data[name] = values
heatmap_center_value = 0
heatmap_color_center = "white"
heatmap_color_up = 0.3
heatmap_color_down = 0.7
heatmap_color_missing = "black"
heatmap_max_value = abs(heatmap_center_value - max_value)
heatmap_min_value = abs(heatmap_center_value - min_value)
if heatmap_center_value <= min_value:
heatmap_max_value = heatmap_min_value + heatmap_max_value
else:
heatmap_max_value = max(heatmap_min_value, heatmap_max_value)
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
f2color = {}
f2last_seed = {}
for node in t.traverse():
node.img_style['size'] = 0
if len(node.children) == 1:
node.img_style['size'] = 2
node.img_style['shape'] = "square"
node.img_style['fgcolor'] = "steelblue"
ftype_pos = defaultdict(int)
for findex, f in enumerate(FACES):
if (f['nodetype'] == 'any' or
(f['nodetype'] == 'leaf' and node.is_leaf()) or
(f['nodetype'] == 'internal' and not node.is_leaf())):
# if node passes face filters
if node_matcher(node, f["filters"]):
if f["value"].startswith("@"):
fvalue = getattr(node, f["value"][1:], None)
else:
fvalue = f["value"]
# if node's attribute has content, generate face
if fvalue is not None:
fsize = f["size"]
fbgcolor = f["bgcolor"]
fcolor = f['color']
if fcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(node, color_keyattr, None)
last_seed = f2last_seed.setdefault(color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(0.1, 0.2)
f2last_seed[color_keyattr] = seed
fcolor = f2color.setdefault(color_bin, random_color(h=seed))
if fbgcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fbgcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(node, color_keyattr, None)
last_seed = f2last_seed.setdefault(color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(0.1, 0.2)
f2last_seed[color_keyattr] = seed
fbgcolor = f2color.setdefault(color_bin, random_color(h=seed))
if f["ftype"] == "text":
if f.get("format", None):
fvalue = f["format"] % fvalue
F = TextFace(fvalue,
fsize = fsize,
fgcolor = fcolor or "black",
fstyle = f.get('fstyle', None))
elif f["ftype"] == "fullseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="seq",
seqtail_format="seq",
height=fsize)
elif f["ftype"] == "compactseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="compactseq",
seqtail_format="compactseq",
height=fsize)
elif f["ftype"] == "blockseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="blockseq",
seqtail_format="blockseq",
height=fsize,
fgcolor=fcolor or "slategrey",
bgcolor=fbgcolor or "slategrey",
scale_factor = 1.0)
fbgcolor = None
elif f["ftype"] == "bubble":
try:
v = float(fvalue)
except ValueError:
rad = fsize
else:
rad = fsize * v
F = faces.CircleFace(radius=rad, style="sphere",
color=fcolor or "steelblue")
elif f["ftype"] == "heatmap":
if not f['column']:
col = ftype_pos[f["pos"]]
else:
col = f["column"]
for i, value in enumerate(heatmap_data.get(node.name, [])):
ftype_pos[f["pos"]] += 1
if value is None:
color = heatmap_color_missing
elif value > heatmap_center_value:
color = gradient_color(abs(heatmap_center_value - value), heatmap_max_value, hue=heatmap_color_up)
elif value < heatmap_center_value:
color = gradient_color(abs(heatmap_center_value - value), heatmap_max_value, hue=heatmap_color_down)
else:
color = heatmap_color_center
node.add_face(RectFace(20, 20, color, color), position="aligned", column=col + i)
# Add header
# for i, name in enumerate(header):
# nameF = TextFace(name, fsize=7)
# nameF.rotation = -90
# tree_style.aligned_header.add_face(nameF, column=i)
F = None
elif f["ftype"] == "profile":
# internal profiles?
F = None
elif f["ftype"] == "barchart":
F = None
elif f["ftype"] == "piechart":
F = None
# Add the Face
if F:
F.opacity = f['opacity'] or 1.0
# Set face general attributes
if fbgcolor:
F.background.color = fbgcolor
if not f['column']:
col = ftype_pos[f["pos"]]
ftype_pos[f["pos"]] += 1
else:
col = f["column"]
node.add_face(F, column=col, position=f["pos"])
if args.image:
t.render("t%d.%s" %(tindex, args.image),
tree_style=ts, w=args.width, h=args.height, units=args.size_units)
else:
t.show(None, tree_style=ts)
def plot_blast_result(tree_file, blast_result_file_list, id2description, id2mlst):
'''
Projet Staph aureus PVL avec Laure Jaton
Script pour afficher une phylog�nie et la conservation de facteurs de firulence c�te � c�te
N�cessite r�sultats MLST, ensemble des r�sultats tblastn (facteurs de virulence vs chromosomes),
ainsi qu'une correspondance entre les accession des g�nomes et les noms qu'on veut afficher dans la phylog�nie. Icemn
pour les identifiants molis des patients, on les remplace par CHUV n.
:param tree_file: phylog�nie au format newick avec identifiants correspondants � tous les dico utilis�s
:param blast_result_file_list: r�sultats tblastn virulence factors vs chromosome (seulement best blast)
:param id2description: identifiants g�nome utiis� dans l'arbre et description correspondante (i.e S aureus Newman)
:param id2mlst: identitifiants arbre 2 S. aureus ST type
:return:
'''
blast2data = {}
queries = []
for one_blast_file in blast_result_file_list:
with open(one_blast_file, 'r') as f:
for line in f:
line = line.split('\t')
if line[1] not in blast2data:
blast2data[line[1]] = {}
blast2data[line[1]][line[0]] = [float(line[2]), int(line[8]), int(line[9])]
else:
blast2data[line[1]][line[0]] = [float(line[2]), int(line[8]), int(line[9])]
if line[0] not in queries:
queries.append(line[0])
print blast2data
print queries
for one_blast in blast2data.keys():
for ref_gene in blast2data[one_blast].keys():
for query_gene in blast2data[one_blast].keys():
overlap = False
if ref_gene == query_gene:
continue
if one_blast == 'NC_002745' and ref_gene == 'selm':
print 'target:', ref_gene, blast2data[one_blast][ref_gene]
print query_gene, blast2data[one_blast][query_gene]
# check if position is overlapping
try:
sorted_coordinates = sorted(blast2data[one_blast][ref_gene][1:3])
if blast2data[one_blast][query_gene][1] <= sorted_coordinates[1] and blast2data[one_blast][query_gene][1]>= sorted_coordinates[0]:
print 'Overlaping locations!'
print one_blast, ref_gene, blast2data[one_blast][ref_gene]
print one_blast, query_gene, blast2data[one_blast][query_gene]
overlap =True
sorted_coordinates = sorted(blast2data[one_blast][query_gene][1:3])
if blast2data[one_blast][ref_gene][1] <= sorted_coordinates[1] and blast2data[one_blast][ref_gene][1]>= sorted_coordinates[0]:
print 'Overlapping locations!'
print one_blast, ref_gene, blast2data[one_blast][ref_gene]
print one_blast, query_gene, blast2data[one_blast][query_gene]
overlap =True
if overlap:
if blast2data[one_blast][ref_gene][0] > blast2data[one_blast][query_gene][0]:
del blast2data[one_blast][query_gene]
print 'removing', query_gene
else:
del blast2data[one_blast][ref_gene]
print 'removing', ref_gene
break
except KeyError:
print 'colocation already resolved:', query_gene, ref_gene
queries_count = {}
for query in queries:
queries_count[query] = 0
for one_blast in blast2data:
if query in blast2data[one_blast]:
queries_count[query]+=1
for query in queries_count:
if queries_count[query] == 0:
queries.pop(queries.index(query))
'''
rm_genes = ['selv','spsmA1','psmB1','psmB2','ses','set','sel','selX','sek','sel2','LukF', 'LukM', 'hly', 'hld'
, 'hlgA', 'hlgB', 'hlgC', 'sed', 'sej', 'ser', 'selq1', 'sec3', 'sek2', 'seq2', 'lukD', 'lukE']
#rm_genes = ['icaR','icaA','icaB','icaC','icaD', 'sdrF', 'sdrH']
for gene in rm_genes:
queries.pop(queries.index(gene))
'''
#queries = ['selv']
t1 = Tree(tree_file)
#t.populate(8)
# Calculate the midpoint node
R = t1.get_midpoint_outgroup()
t1.set_outgroup(R)
t1.ladderize()
#t2=t1
#for lf in t2.iter_leaves():
# try:
# lf.name = ' %s (%s)' % (id2description[lf.name], id2mlst[lf.name])
# except:
# #lf.name = ' %s (%s)' % (lf.name, lf.name)
#
# a = TextFace(' %s (%s)' % (lf.name, id2mlst[lf.name]))
# a.fgcolor = "red"
# lf.name = a
#t2.render("test.svg", dpi=800, h=400)
#import sys
#sys.exit()
# and set it as tree outgroup
head = True
for lf in t1.iter_leaves():
#lf.add_face(AttrFace("name", fsize=20), 0, position="branch-right")
lf.branch_vertical_margin = 0
#data = [random.randint(0,2) for x in xrange(3)]
for col, value in enumerate(sorted(queries)):
print lf.name, value
if head:
'first row, print gene names'
#print 'ok!'
n = TextFace(' %s ' % str(value))
n.margin_top = 4
n.margin_right = 4
n.margin_left = 4
n.margin_bottom = 4
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col, position="aligned")
try:
identity_value = blast2data[lf.name][value][0]
if 'nord' in id2description[lf.name]:
if float(identity_value) >70:
if str(identity_value) == '100.00' or str(identity_value) == '100.0':
identity_value = '100'
else:
identity_value = str(round(float(identity_value), 1))
n = TextFace(' %s ' % str(identity_value))
n.margin_top = 4
n.margin_right = 4
n.margin_left = 4
n.margin_bottom = 4
n.inner_background.color = rgb2hex(m.to_rgba(float(identity_value)))
if float(identity_value) >92:
n.fgcolor = "white"
n.opacity = 1.
lf.add_face(n, col, position="aligned")
else:
identity_value = '-'
n = TextFace(' %s ' % str(identity_value))
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col, position="aligned")
else:
if float(identity_value) >70:
if str(identity_value) == '100.00' or str(identity_value) == '100.0':
identity_value = '100'
else:
identity_value = str(round(float(identity_value), 1))
n = TextFace(' %s ' % str(identity_value))
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = rgb2hex(m2.to_rgba(float(identity_value)))
if float(identity_value) >92:
n.fgcolor = "white"
n.opacity = 1.
lf.add_face(n, col, position="aligned")
else:
identity_value = '-'
n = TextFace(' %s ' % str(identity_value))
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col, position="aligned")
except KeyError:
identity_value = '-'
n = TextFace(' %s ' % str(identity_value))
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col, position="aligned")
try:
lf.name = ' %s (%s)' % (id2description[lf.name], id2mlst[lf.name])
except:
#lf.name = ' %s (%s)' % (lf.name, lf.name)
a = TextFace(' %s (%s)' % (lf.name, id2mlst[lf.name]))
a.fgcolor = "red"
lf.name = a
head = False
#.add_face(a, 0, position="aligned")
# add boostrap suppot
#for n in t1.traverse():
# if n.is_leaf():
# continue
# n.add_face(TextFace(str(t1.support)), column=0, position = "branch-bottom")
#ts = TreeStyle()
#ts.show_branch_support = True
# , tree_style=ts
t1.render("test.svg", dpi=800, h=400)
def plot_blast_result(tree_file,
blast_result_file_list,
id2description,
id2mlst,
check_overlap,
ordered_queries,
fasta_file2accession,
id_cutoff=80,
reference_accession='-',
accession2hit_filter=False,
show_identity_values=True):
'''
Projet Staph aureus PVL avec Laure Jaton
Script pour afficher une phylogénie et la conservation de facteurs de virulence côte à côte
Nécessite résultats MLST, ensemble des résultats tblastn (facteurs de virulence vs chromosomes),
ainsi qu'une correspondance entre les accession des génomes et les noms qu'on veut afficher dans la phylogénie. Icemn
pour les identifiants molis des patients, on les remplace par CHUV n.
:param tree_file: phylogénie au format newick avec identifiants correspondants à tous les dico utilisés
:param blast_result_file_list: résultats tblastn virulence factors vs chromosome (seulement best blast)
:param id2description: identifiants génome utiisé dans l'arbre et description correspondante (i.e S aureus Newman)
:param id2mlst: identitifiants arbre 2 S. aureus ST type
:return:
'''
import blast_utils
blast2data, queries = blast_utils.remove_blast_redundancy(
blast_result_file_list, check_overlap)
queries_count = {}
for query in queries:
queries_count[query] = 0
for one_blast in blast2data:
if query in blast2data[one_blast]:
#print blast2data[one_blast][query]
if float(blast2data[one_blast][query][0]) > id_cutoff:
queries_count[query] += 1
else:
del blast2data[one_blast][query]
print queries_count
for query in queries:
print "Hit counts: %s\t%s" % (query, queries_count[query])
if queries_count[query] == 0:
queries.pop(queries.index(query))
print 'delete columns with no matches ok'
'''
rm_genes = ['selv','spsmA1','psmB1','psmB2','ses','set','sel','selX','sek','sel2','LukF', 'LukM', 'hly', 'hld'
, 'hlgA', 'hlgB', 'hlgC', 'sed', 'sej', 'ser', 'selq1', 'sec3', 'sek2', 'seq2', 'lukD', 'lukE']
#rm_genes = ['icaR','icaA','icaB','icaC','icaD', 'sdrF', 'sdrH']
for gene in rm_genes:
queries.pop(queries.index(gene))
'''
#queries = ['selv']
t1 = Tree(tree_file)
tss = TreeStyle()
#tss.show_branch_support = True
# Calculate the midpoint node
R = t1.get_midpoint_outgroup()
t1.set_outgroup(R)
t1.ladderize()
ordered_queries_filtered = []
for query in ordered_queries:
hit_count = 0
for lf2 in t1.iter_leaves():
try:
accession = fasta_file2accession[lf2.name]
tmpidentity = blast2data[accession][query][0]
if float(tmpidentity) > float(id_cutoff):
hit_count += 1
except:
continue
if hit_count > 0:
ordered_queries_filtered.append(query)
#print 'skippink-----------'
head = True
print 'drawing tree'
print 'n initial queries: %s n kept: %s' % (len(ordered_queries),
len(ordered_queries_filtered))
for lf in t1.iter_leaves():
#lf.add_face(AttrFace("name", fsize=20), 0, position="branch-right")
lf.branch_vertical_margin = 0
#data = [random.randint(0,2) for x in xrange(3)]
accession = fasta_file2accession[lf.name]
for col, value in enumerate(ordered_queries_filtered):
if head:
if show_identity_values:
#'first row, print gene names'
#print 'ok!'
n = TextFace(' %s ' % str(value))
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.rotation = 270
n.vt_align = 2
n.hz_align = 2
n.inner_background.color = "white"
n.opacity = 1.
#lf.add_face(n, col, position="aligned")
tss.aligned_header.add_face(n, col)
else:
n = TextFace(' %s ' % str(value), fsize=6)
n.margin_top = 0
n.margin_right = 0
n.margin_left = 0
n.margin_bottom = 0
n.rotation = 270
n.vt_align = 2
n.hz_align = 2
n.inner_background.color = "white"
n.opacity = 1.
#lf.add_face(n, col, position="aligned")
tss.aligned_header.add_face(n, col)
try:
identity_value = blast2data[accession][value][0]
#print 'identity', lf.name, value, identity_value
if lf.name != reference_accession:
if not accession2hit_filter:
# m_red
color = rgb2hex(m_blue.to_rgba(float(identity_value)))
else:
# if filter, color hits that are not in the filter in green
if accession in accession2hit_filter:
if value in accession2hit_filter[accession]:
# mred
color = rgb2hex(
m_green.to_rgba(float(identity_value)))
else:
color = rgb2hex(
m_blue.to_rgba(float(identity_value)))
else:
color = rgb2hex(
m_blue.to_rgba(float(identity_value)))
else:
# reference taxon, blue scale
color = rgb2hex(m_blue.to_rgba(float(identity_value)))
#if not show_identity_values:
# color = rgb2hex(m_blue.to_rgba(float(identity_value)))
except:
identity_value = 0
color = "white"
if show_identity_values:
if float(identity_value) >= float(id_cutoff):
if str(identity_value) == '100.00' or str(
identity_value) == '100.0':
identity_value = '100'
n = TextFace("%s " % identity_value)
else:
# identity_value = str(round(float(identity_value), 1))
n = TextFace("%.2f" % round(float(identity_value), 2))
if float(identity_value) > 95:
n.fgcolor = "white"
n.opacity = 1.
else:
identity_value = '-'
n = TextFace(' %s ' % str(identity_value))
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = color
lf.add_face(n, col, position="aligned")
else:
if float(identity_value) >= float(id_cutoff):
# don't show identity values
n = TextFace(' ')
n.margin_top = 0
n.margin_right = 0
n.margin_left = 0
n.margin_bottom = 0
#n.color = color
n.inner_background.color = color
lf.add_face(n, col, position="aligned")
try:
accession = fasta_file2accession[lf.name]
lf.name = ' %s (%s)' % (id2description[accession],
id2mlst[lf.name])
except KeyError:
print '--------', id2description
lf.name = ' %s (%s)' % (lf.name, id2mlst[lf.name])
head = False
for n in t1.traverse():
nstyle = NodeStyle()
if n.support < 0.9:
#mundo = TextFace("%s" % str(n.support))
#n.add_face(mundo, column=1, position="branch-bottom")
nstyle["fgcolor"] = "blue"
nstyle["size"] = 6
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
print 'rendering tree'
t1.render("profile.svg", dpi=1000, h=400, tree_style=tss)
