def get_example_tree():
# Performs a tree reconciliation analysis
gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
t = PhyloTree(gene_tree_nw)
ts = TreeStyle()
# disable default PhyloTree Layout
ts.layout_fn = lambda x: True
t.link_to_alignment(alg)
node2content = t.get_cached_content()
for node in t.traverse():
node.img_style["size"] = 0
if not node.is_leaf():
leaves = node2content[node]
# get columns with different aa
subseqs, relevant_columns = mutation_columns([lf.sequence for lf in leaves])
for seq in subseqs:
f = SeqMotifFace(seq, seq_format="seq", width=10, height=8)
f.margin_top = 2
f.margin_right = 6
node.add_face(f, column=0, position="branch-bottom")
for j, col in enumerate(relevant_columns):
col_f = RectFace(10, 10, fgcolor=None, bgcolor=None,
label={"text":str(col), "fonttype":"Courier", "color":"black", "fontsize":6})
node.add_face(col_f, column=j, position="branch-top")
col_f.margin_bottom = 2
else:
f = SeqMotifFace(node.sequence, seq_format="seq", width=6)
node.add_face(f, column=0, position="aligned")
alg_length = len(lf.sequence)
ts.draw_aligned_faces_as_table = False
for colnum in xrange(alg_length):
col_f = RectFace(10, 10, fgcolor=None, bgcolor=None,
label={"text":str(colnum), "fonttype":"Courier", "color":"black", "fontsize":6})
ts.aligned_header.add_face(col_f, column=colnum)
return t, ts
"""
# Load a tree and link it to an alignment. As usual, 'alignment' can
# be the path to a file or data in text format.
t = PhyloTree("(((seqA,seqB),seqC),seqD);", alignment=fasta_txt, alg_format="fasta")
#We can now access the sequence of every leaf node
print "These are the nodes and its sequences:"
for leaf in t.iter_leaves():
print leaf.name, leaf.sequence
#seqD MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
#seqC MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
#seqA MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
#seqB MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
#
# The associated alignment can be changed at any time
t.link_to_alignment(alignment=iphylip_txt, alg_format="iphylip")
# Let's check that sequences have changed
print "These are the nodes and its re-linked sequences:"
for leaf in t.iter_leaves():
print leaf.name, leaf.sequence
#seqD MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAHQ----------FMALTNVSH
#seqC MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAHQFMALTNVSH----------
#seqA MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQFMALTNVSHQFMALTNVSH
#seqB MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAHQFMALTNVSH----------
#
# The sequence attribute is considered as node feature, so you can
# even include sequences in your extended newick format!
print t.write(features=["sequence"], format=9)
#
#
# (((seqA[&&NHX:sequence=MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQF
def uploaded_secuence(request):
path = BASE_DIR + '/secuences/secuence.fasta'
handler = SequenceHandler()
handler.validate_sequences(path)
upload_id = calendar.timegm(time.gmtime())
if not handler.has_errors:
for fasta in handler.dic_data:
coordenadas = convertDirectionToCoordinates(fasta['loc'])
fasta_to_insert = Secuence()
fasta_to_insert.address = fasta['loc']
fasta_to_insert.date = fasta['date']
fasta_to_insert.latitud = coordenadas[0]
fasta_to_insert.longitud = coordenadas[1]
fasta_to_insert.bio_id = fasta['gb']
fasta_to_insert.content = fasta['seq']
fasta_to_insert.length = len(fasta['seq'])
fasta_to_insert.upload_id = upload_id
fasta_to_insert.source = fasta['source']
fasta_to_insert.save()
handler.clean_data()
if not handler.is_aligned:
if platform.system() == 'Linux':
handler.lnx_alignment(path)
handler.lnx_build_tree()
else:
handler.win_alignment(path)
handler.win_build_tree()
else:
# la secuencia esta alineada
handler.make_file_aln_for_iqtree()
if platform.system() == 'Linux':
handler.lnx_build_tree()
else:
handler.win_build_tree()
messages.success(request, f"El archivo se ha subido correctamente")
tree_file = BASE_DIR + "/secuences/secuence.fasta_aln.fasta.treefile"
aln_path = BASE_DIR + "/secuences/secuence.fasta_aln.fasta"
ts = TreeStyle()
ts.force_topology = True
ts.show_branch_support = True
ts.show_leaf_name = False
ts.branch_vertical_margin = 10
t = PhyloTree(tree_file)
t.link_to_alignment(aln_path)
img_name = "TpFinalBioApp/static/TpFinalBioApp/img/output/myTree" + "_" + str(
upload_id) + ".svg"
t.render(img_name, tree_style=ts)
print(t)
if platform.system() != 'Linux':
os.remove(BASE_DIR +
"/secuences/secuence.fasta_aln.fasta.model.gz")
return redirect('Map', upload_id)
else:
messages.error(request,
f"El archivo no es correcto. " + handler.error_message)
return redirect('Home')
# Performs a tree reconciliation analysis
gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
species_tree_nw = "((((Hsa, Ptr), Mmu), (Mms, Cfa)), Dme);"
genetree = PhyloTree(gene_tree_nw)
sptree = PhyloTree(species_tree_nw)
recon_tree, events = genetree.reconcile(sptree)
recon_tree.link_to_alignment(alg)
return recon_tree, TreeStyle()
if __name__ == "__main__":
# Visualize the reconciled tree
t, ts = get_example_tree()
t.show(tree_style=ts)
#recon_tree.render("phylotree.png", w=750)
fasta_txt = """
>seqA
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
>seqB
MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
>seqC
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
>seqD
MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
"""
# Load a tree and link it to an alignment.
t = PhyloTree("(((seqA,seqB),seqC),seqD);")
t.link_to_alignment(alignment=fasta_txt, alg_format="fasta")
t.show()
# be the path to a file or data in text format.
t = PhyloTree("(((seqA,seqB),seqC),seqD);",
alignment=fasta_txt,
alg_format="fasta")
#We can now access the sequence of every leaf node
print "These are the nodes and its sequences:"
for leaf in t.iter_leaves():
print leaf.name, leaf.sequence
#seqD MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
#seqC MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
#seqA MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
#seqB MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
#
# The associated alignment can be changed at any time
t.link_to_alignment(alignment=iphylip_txt, alg_format="iphylip")
# Let's check that sequences have changed
print "These are the nodes and its re-linked sequences:"
for leaf in t.iter_leaves():
print leaf.name, leaf.sequence
#seqD MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAHQ----------FMALTNVSH
#seqC MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAHQFMALTNVSH----------
#seqA MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQFMALTNVSHQFMALTNVSH
#seqB MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAHQFMALTNVSH----------
#
# The sequence attribute is considered as node feature, so you can
# even include sequences in your extended newick format!
print t.write(features=["sequence"], format=9)
#
#
# (((seqA[&&NHX:sequence=MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQF
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "nt",
fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if __name__ == "__main__":
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment("""
>Chimp
HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
>Orangutan
DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
>Human
DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
""")
nt_sequences = {"Human" : "GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG",
"Chimp" : "CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG",
"Orangutan": "GATGCACGCTGGATCAACGAAAAGTTAAGATGCGTATCGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGGAGTAAGTCAATACGTTAAAGGTCGTCCG"
}
for l in nt_sequences:
(tree & l).nt_sequence = nt_sequences[l]
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace("Example for nucleotides...", fsize=15), column=0)
ts.layout_fn = test_layout_evol
tree.show(tree_style=ts)
def make_tree_ali_detect_combi(g_tree,
ali_nf,
Out,
hist_up="",
x_values=[],
hp=[],
dict_benchmark={},
reorder=False,
det_tool=False,
title=""):
reptree = g_tree.reptree
cz_nodes = g_tree.cz_nodes
### Tree
## Tree style
phylotree_style = TreeStyle()
phylotree_style.show_leaf_name = False
phylotree_style.show_branch_length = False
phylotree_style.draw_guiding_lines = True
phylotree_style.min_leaf_separation = 1
## For noisy tree
cz_nodes_s = {}
if cz_nodes:
cols = [
"#008000", "#800080", "#007D80", "#9CA1A2", "#A52A2A", "#ED8585",
"#FF8EAD", "#8EB1FF", "#FFE4A1", "#ADA1FF"
]
col_i = 0
for Cz in cz_nodes.keys():
cz_nodes_s[Cz] = NodeStyle()
cz_nodes_s[Cz]["fgcolor"] = cols[col_i]
cz_nodes_s[Cz]["size"] = 5
cz_nodes_s[Cz]["hz_line_width"] = 2
cz_nodes_s[Cz]["vt_line_width"] = 2
cz_nodes_s[Cz]["vt_line_color"] = cols[col_i]
cz_nodes_s[Cz]["hz_line_color"] = cols[col_i]
col_i += 1
sim_root_ND = g_tree.outgroup_ND
def my_layout(node):
## Sequence name
F = TextFace(node.name, tight_text=True)
add_face_to_node(F, node, column=0, position="aligned")
## Sequence motif
if node.is_leaf():
motifs_n = []
box_color = "black"
opacity = 1
if node.T == "True" or node.C == "True":
motifs_n.append([
0,
len(node.sequence), "[]", 10, 12, box_color, box_color,
None
])
motifs_n.append(
[0, len(node.sequence), "seq", 10, 10, None, None, None])
seq_face = SeqMotifFace(seq=node.sequence,
seqtype='aa',
seq_format='seq',
fgcolor=box_color,
motifs=motifs_n)
seq_face.overlaping_motif_opacity = opacity
add_face_to_node(seq_face, node, column=1, position='aligned')
## Nodes style
if det_tool and node.T == "True":
node.set_style(nstyle_T_sim)
add_t(node)
elif det_tool and node.C == "True":
node.set_style(nstyle_C_sim)
elif det_tool:
node.set_style(nstyle)
#if not det_tool no background
elif node.T == "True" and not int(
node.ND) in g_tree.conv_events.nodesWithTransitions_est:
node.set_style(nstyle_T_sim)
add_t(node)
elif node.T == "True" and int(
node.ND) in g_tree.conv_events.nodesWithTransitions_est:
node.set_style(nstyle_T_sim_est)
add_t(node)
elif int(node.ND) in g_tree.conv_events.nodesWithTransitions_est:
node.set_style(nstyle_T_est)
elif node.C == "True" and not int(
node.ND) in g_tree.conv_events.nodesWithConvergentModel_est:
node.set_style(nstyle_C_sim)
elif node.C == "True" and int(
node.ND) in g_tree.conv_events.nodesWithConvergentModel_est:
node.set_style(nstyle_C_sim_est)
elif int(node.ND) in g_tree.conv_events.nodesWithConvergentModel_est:
node.set_style(nstyle_C_est)
elif cz_nodes_s and node.Cz != "False":
node.set_style(cz_nodes_s[int(node.Cz)])
if int(node.ND) == int(cz_nodes[int(node.Cz)][0]):
add_t(node)
else:
node.set_style(nstyle)
if int(node.ND) == sim_root_ND and not det_tool:
add_sim_root(node)
phylotree_style.layout_fn = my_layout
# Get tree dimensions
tree_nf = g_tree.annotated_tree_fn_est
logger.debug("tree_nf: %s", tree_nf)
t = PhyloTree(tree_nf)
t.link_to_alignment(ali_nf)
t.render(Out)
tree_face = TreeFace(t, phylotree_style)
tree_face.update_items()
tree_h = tree_face._height()
tree_w = tree_face._width()
### X axes:
if not x_values: # Complete representation
x_values_up = [
x + 1 for x in range(0, len(dict_benchmark.values()[0]))
]
inter = 5
else: # Filtered representation
x_values_up = x_values
inter = 1
### Histogram up
if hist_up in ["PCOC", "PC", "OC", "Topological", "Identical"]:
header_hist_value_up = 'Posterior probability (' + hist_up.upper(
) + ' model)'
hist_value_up = dict_benchmark[hist_up]
# Define emphased lines
hlines = [0.8, 0.9, 0.99]
hlines_col = ['#EFDB00', 'orange', 'red']
# Type of representation
kind = 'stick' # bar/curve/stick
y_values_up = hist_value_up
hist = SequencePlotFace_mod(y_values_up,
hlines=hlines,
hlines_col=hlines_col,
kind=kind,
header=header_hist_value_up,
height=40,
col_width=10,
ylim=[0, 1])
hist.hp = hp
hist.x_values = x_values_up
hist.x_inter_values = inter
hist.set_sticks_color()
if reorder:
# draw colored boxes
hist.put_colored_boxes = (True, tree_h + 40)
phylotree_style.aligned_header.add_face(hist, 1)
### Rect all model:
sequencescorebox = SequenceScoreFace(dict_benchmark, col_width=10)
sequencescorebox.hp = hp
sequencescorebox.x_values = x_values_up
sequencescorebox.x_inter_values = inter
if not hist_up in ["PCOC", "PC", "OC", "Topological", "Identical"]:
sequencescorebox.x_axis = True
phylotree_style.aligned_header.add_face(sequencescorebox, 1)
if title:
phylotree_style.title.add_face(TextFace(title), column=0)
tree_nf = reptree + "/annotated_tree.nhx"
logger.debug("tree_nf: %s", tree_nf)
res = t.render(Out, tree_style=phylotree_style)
del t
return (res)
def getPhyloTree(self):
# Performs a tree reconciliation analysis
gene_tree_nw = self.newick
genetree = PhyloTree(gene_tree_nw)
genetree.link_to_alignment(self.alg)
return genetree, TreeStyle()
if node.is_leaf():
if hasattr(node, "sequence"):
seqface = MySequenceFace(node.sequence,
"nt",
fsize=10,
col_w=11,
interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if __name__ == "__main__":
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment("""
>Chimp
HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
>Orangutan
DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
>Human
DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
""")
nt_sequences = {
"Human":
"GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG",
"Chimp":
"CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG",
"Orangutan":
"GATGCACGCTGGATCAACGAAAAGTTAAGATGCGTATCGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGGAGTAAGTCAATACGTTAAAGGTCGTCCG"
}
for l in nt_sequences:
(tree & l).nt_sequence = nt_sequences[l]
tree.dist = 0
ts = TreeStyle()
