def phylogenetic_tree(extant_taxa, branch_lengths=(.01, .5)):
names_as_strings = [str(i) for i in range(extant_taxa)]
tree = PhyloTree(format=1)
tree.populate(extant_taxa,
random_branches=True,
branch_range=branch_lengths,
names_library=names_as_strings)
tree.dist = 0
current_name = 2 * extant_taxa - 2
for node in tree.traverse('preorder'):
if not node.is_leaf():
node.name = str(current_name)
current_name -= 1
return tree
def process_tree(treepath):
''' processes a tree to extract orthology relationships between target taxid and the rest
of species, organized by orthology type and species code '''
treepath = str(treepath)
treepath = treepath.rstrip()
t = PhyloTree(treepath, sp_naming_function=get_species)
# traverse all leaves in tree file and get taxid
leaf_count = 0
for leaf in t:
leaf_count += 1
tax = int(leaf.name.split(".", 1)[0])
#get scientific name and convert taxid from int to str
sci_name = names.get(tax)
leaf.taxid = str(tax)
#rename leaves names
try:
good_name = "%s" % (conversion[leaf.name][0])
except:
good_name = leaf.name
good_name = re.sub("[ |\t,:)(;\n\]\[]+", "_", good_name)
leaf.good_name = good_name
#obtain cluster name from tree file path
clus_name = os.path.split(treepath)[-1].replace(".fa.final_tree.nw", "")
try:
base_name = conversion[clus_name][0].replace('|', '_')
except:
base_name = clus_name[0]
t.dist = 0
#colapses plat specific
node2content = t.get_cached_content()
target_species = set([target_taxid])
def is_sp_specific(_node):
_species = set([_leaf.species for _leaf in node2content[_node]])
if not (_species - target_species):
return True
return False
#traverse only lamprey leaves
if collapse == 'yes':
for n in t.get_leaves(is_leaf_fn=is_sp_specific):
if n.children:
for ch in n.get_children():
ch.detach()
n.taxid = target_taxid
n.name = "%s" % ('|'.join(
[_lf.name for _lf in node2content[n]]))
n.good_name = "{%s}" % ('|'.join(
[_lf.good_name for _lf in node2content[n]]))
#set outgroup
outgroup = t.get_midpoint_outgroup()
try:
t.set_outgroup(outgroup)
except:
if len(t) == 1:
return
else:
raise
node2content = t.get_cached_content()
event_lines = []
for ev in t.get_descendant_evol_events():
if ev.etype == "S":
source_seqs = node2content[ev.node.children[0]]
ortho_seqs = node2content[ev.node.children[1]]
sp_1 = set()
for leaf in source_seqs:
sp_1.add(leaf.taxid)
sp_2 = set()
for leaf in ortho_seqs:
sp_2.add(leaf.taxid)
if str(target_taxid) in sp_1:
source_seqs, ortho_seqs = source_seqs, ortho_seqs
elif str(target_taxid) in sp_2:
source_seqs, ortho_seqs = ortho_seqs, source_seqs
else:
continue
#co_orthologs is a list with lamprey seed in source_seqs
co_orthologs = [
leaf.good_name for leaf in source_seqs
if leaf.taxid == str(target_taxid)
]
co_orthologs.sort()
#orthologs is a list of all ortho_seqs names
orthologs = defaultdict(set)
for leaf in ortho_seqs:
sp = int(leaf.taxid)
orthologs[sp].add(leaf.good_name)
if len(co_orthologs) == 1:
_otype = "one-to-"
else:
_otype = "many-to-"
for sp, orth in orthologs.iteritems():
if len(orth) == 1:
otype = _otype + "one"
else:
otype = _otype + "many"
event_lines.append('\t'.join([
','.join(co_orthologs), otype,
str(sp), names[sp], ','.join(sorted(orth)), '\n'
]))
return event_lines
def process_tree(treepath):
''' processes a tree to extract orthology relationships between target taxid and the rest
of species, organized by orthology type and species code '''
treepath = str(treepath)
treepath = treepath.rstrip()
t = PhyloTree(treepath, sp_naming_function=get_species)
treefile = os.path.basename(treepath)
t.dist = 0
outgroup = t.get_midpoint_outgroup()
try:
t.set_outgroup(outgroup)
t.standardize()
except:
if args.pairs_table:
if len(t) == 1:
sys.stderr.write(treefile + 'len(t) == 1' + '\n')
return ([], [])
#return (['aa', 'aa'] ,[['aa', 'aa']])
else:
sys.stderr.write(treefile + 'len(t) != 1' + '\n')
l = t.get_leaf_names()
r = l[0]
t.set_outgroup(r)
pass
#return ([],[])
#return (['None', 'None'] ,[['None', 'None']])
else:
if len(t) == 1:
sys.stderr.write(treefile + 'len(t) == 1' + '\n')
return []
else:
sys.stderr.write(treefile + 'len(t) != 1' + '\n')
return []
names = {}
for leaf in t:
try:
sp = str(leaf.name.split('.')[0])
leaf.taxid = str(sp)
sci_name = ncbi.get_taxid_translator([sp])
names[sp] = sci_name[int(sp)]
except:
names[sp] = ''
if args.conv_table:
try:
good_name = "%s" % (conversion[leaf.name][0])
except:
good_name = leaf.name
leaf.good_name = good_name
node2content = t.get_cached_content()
target_species = set([target_taxid])
def is_sp_specific(_node):
_species = set([_leaf.species for _leaf in node2content[_node]])
if not (_species - target_species):
return True
return False
#traverse only target taxid leaves
if collapse == 'yes':
for n in t.get_leaves(is_leaf_fn=is_sp_specific):
if n.children:
for ch in n.get_children():
ch.detach()
n.taxid = target_taxid
n.name = "{%s}" % ('|'.join(
[_lf.name for _lf in node2content[n]]))
if args.conv_table:
n.good_name = "{%s}" % ('|'.join(
[_lf.good_name for _lf in node2content[n]]))
all_ortholgs_tree = []
all_ortholgs_pairs = []
event_lines = []
for ev in t.get_descendant_evol_events():
if ev.etype == "S":
source_seqs = ev.node.children[0]
ortho_seqs = ev.node.children[1]
if target_taxid:
sp_1 = set()
for leaf in source_seqs:
sp_1.add(leaf.taxid)
sp_2 = set()
for leaf in ortho_seqs:
sp_2.add(leaf.taxid)
if str(target_taxid) in sp_1:
source_seqs, ortho_seqs = source_seqs, ortho_seqs
elif str(target_taxid) in sp_2:
source_seqs, ortho_seqs = ortho_seqs, source_seqs
else:
continue
if args.conv_table:
co_orthologs = [leaf.good_name for leaf in source_seqs]
co_orthologs.sort()
else:
co_orthologs = [leaf.name for leaf in source_seqs]
co_orthologs.sort()
orthologs = defaultdict(set)
for leaf in ortho_seqs:
sp = str(leaf.name.split('.')[0])
if args.conv_table:
orthologs[sp].add(leaf.good_name)
else:
orthologs[sp].add(leaf.name)
if len(source_seqs) == 1:
_otype = "one-to-"
else:
_otype = "many-to-"
for sp, orth in orthologs.items():
if len(orth) == 1:
otype = _otype + "one"
else:
otype = _otype + "many"
event_lines.append('\t'.join([
','.join(co_orthologs), otype,
str(sp), ','.join(sorted(orth)), treefile, names[sp], '\n'
]))
if args.pairs_table:
source_seqs_names = []
ortho_seqs_names = []
for node in source_seqs:
for leaf in node:
if args.conv_table:
name = leaf.good_name
else:
name = leaf.name
source_seqs_names.append(name)
for node in ortho_seqs:
for leaf in node:
if args.conv_table:
name = leaf.good_name
else:
name = leaf.name
ortho_seqs_names.append(name)
all_ortholgs_node = itertools.product(source_seqs_names,
ortho_seqs_names)
all_ortholgs_tree.append(all_ortholgs_node)
for node in all_ortholgs_tree:
for pair in node:
all_ortholgs_pairs.append(pair)
#return (event_lines, all_ortholgs_pairs)
if args.pairs_table:
return (event_lines, all_ortholgs_pairs)
else:
return (event_lines)
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)
# Show very large algs
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment(">Human\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Chimp\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Orangutan\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]))
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace("better not set interactivity if alg is very large", fsize=15), column=0)
ts.layout_fn = test_layout_phylo_aa
>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)
# Show very large algs
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment(">Human\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Chimp\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Orangutan\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]))
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace(
"better not set interactivity if alg is very large", fsize=15),
