def read_dlcoal_recon(filename, stree,
exts={"coal_tree": ".coal.tree",
"coal_recon": ".coal.recon",
"locus_tree": ".locus.tree",
"locus_recon": ".locus.recon",
"daughters": ".daughters"
},
filenames={}):
"""Reads a reconciled gene tree from files"""
extra = {}
# trees
coal_tree = treelib.read_tree(
filenames.get("coal_tree", filename + exts["coal_tree"]))
extra["locus_tree"] = treelib.read_tree(
filenames.get("locus_tree", filename + exts["locus_tree"]))
# recons
extra["coal_recon"], junk = phylo.read_recon_events(
filenames.get("coal_recon", filename + exts["coal_recon"]),
coal_tree, extra["locus_tree"])
extra["locus_recon"], extra["locus_events"] = phylo.read_recon_events(
filenames.get("locus_recon", filename + exts["locus_recon"]),
extra["locus_tree"], stree)
extra["daughters"] = set(
extra["locus_tree"].nodes[x] for x in util.read_strings(
filenames.get("daughters", filename + exts["daughters"])))
return coal_tree, extra
def read(self, filename, stree,
exts={"coal_tree": ".coal.tree",
"coal_recon": ".coal.recon",
"locus_tree": ".locus.tree",
"locus_recon": ".locus.recon",
"daughters": ".daughters"
},
filenames={},
check=True):
"""Reads a reconciled gene tree from files"""
# trees
coal_tree = treelib.read_tree(
filenames.get("coal_tree", filename + exts["coal_tree"]))
self.locus_tree = treelib.read_tree(
filenames.get("locus_tree", filename + exts["locus_tree"]))
# recons
self.coal_recon, junk = phylo.read_recon_events(
filenames.get("coal_recon", filename + exts["coal_recon"]),
coal_tree, self.locus_tree)
self.locus_recon, self.locus_events = phylo.read_recon_events(
filenames.get("locus_recon", filename + exts["locus_recon"]),
self.locus_tree, stree)
self.daughters = set(
self.locus_tree.nodes[x] for x in util.read_strings(
filenames.get("daughters", filename + exts["daughters"])))
assert (not check) or (check and self.is_valid(coal_tree))
return coal_tree, self.get_dict()
def read(
self,
filename,
stree,
exts={
"coal_tree": ".coal.tree",
"coal_recon": ".coal.recon",
"locus_tree": ".locus.tree",
"locus_recon": ".locus.recon",
"daughters": ".daughters"
},
filenames={},
check=True):
"""Reads a reconciled gene tree from files"""
# trees
coal_tree = treelib.read_tree(
filenames.get("coal_tree", filename + exts["coal_tree"]))
self.locus_tree = treelib.read_tree(
filenames.get("locus_tree", filename + exts["locus_tree"]))
# recons
self.coal_recon, junk = phylo.read_recon_events(
filenames.get("coal_recon", filename + exts["coal_recon"]),
coal_tree, self.locus_tree)
self.locus_recon, self.locus_events = phylo.read_recon_events(
filenames.get("locus_recon", filename + exts["locus_recon"]),
self.locus_tree, stree)
self.daughters = set(
self.locus_tree.nodes[x] for x in util.read_strings(
filenames.get("daughters", filename + exts["daughters"])))
assert (not check) or (check and self.is_valid(coal_tree))
return coal_tree, self.get_dict()
#gene2species = phylo.read_gene2species(conf.smap)
stree = treelib1.read_tree(conf.stree)
tree = treelib1.read_tree(conf.tree)
if conf.names:
snames = dict(util.read_delim(conf.names))
else:
snames = None
if conf.brecon:
brecon = phylo.read_brecon(conf.brecon, tree, stree)
elif conf.recon:
recon, events = phylo.read_recon_events(conf.recon, tree, stree)
brecon = phylo.recon_events2brecon(recon, events)
else:
gene2species = phylo.read_gene2species(conf.smap)
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
brecon = phylo.recon_events2brecon(recon, events)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
transsvg.draw_tree(tree, brecon, stree, filename=conf.output,
snames=snames)
def hemiplasyConditions(numFamilies = 5351,
dataPath = '/home/muddcs15/research/work/hemiplasy/data/real-fungi/',
outputFile = '/home/muddcs15/research/work/hemiplasy/results/hemiplasy-loss.txt',
spectree = '/home/muddcs15/research/work/hemiplasy/data/config/fungi.stree'):
# create variables and output file
output = open(outputFile,'w')
count = 0
# define a list of all species and lists of each of the species pairs in separate lists
stree = treelib.read_tree(spectree) # species tree
species = stree.leaf_names()
species1 = []
species2 = []
for node in stree:
if len(node.leaves()) == 2:
species1.append(node.children[0].name)
species2.append(node.children[1].name)
# loop over each fam id
for famid in xrange(numFamilies):
flag = False # this families met the criteria for possible hemiplasy
locus_dict = collections.defaultdict(list) # key = locus number, val = list of (gn, sp) in the locus
famFilename = dataPath + '%d/%d-dup.dlcoal.dlcpar.recon' % (famid,famid)
# if the file is not empty, process it
if os.stat(famFilename).st_size != 0:
# read the locus tree and the reconcilitation file
tree_filename = dataPath + '%d/%d.dlcoal.locus.tree' % (famid,famid)
recon_filename = dataPath + '%d/%d.dlcoal.locus.recon' % (famid,famid)
tree = treelib.read_tree(tree_filename) # locus tree
recon, events = phylo.read_recon_events(recon_filename, tree, stree) # reconciliation and events
# create a dictionary for [locus] = species tree location
locus_sname = {}
# find location in species tree where each locus was created and then close dlcpar file
dupFilename = dataPath + '%d/%d.dlcoal.dlcpar.dup.rel.txt' % (famid,famid)
for line in util.open_stream(dupFilename):
locus, gns1, gns2, sname = line.rstrip().split('\t')
locus_sname[locus] = sname
# track to genes and species in each locus
for line in util.open_stream(famFilename):
# assign names to the columns in the file
gn, sp, locus = line.rstrip().split('\t')
if locus == "1":
continue
# store dict of key = locus, val = list of (gene, species) in locus
locus_dict[locus].append((gn, sp))
# for each locus, determine if genes in locus satisfy the properties for a possible hemiplasy
for locus, lst in locus_dict.iteritems():
sps = [sp for (gn,sp) in lst]
gns = [gn for (gn,sp) in lst]
# check if exists in only one species in a pair
for sp1, sp2 in zip(species1, species2):
if (sp1 in sps and sp2 not in sps) or \
(sp2 in sps and sp1 not in sps):
# check if exists elsewhere (outside pair)
for allsp in species:
if (allsp != sp1) and (allsp != sp2) and (allsp in sps):
flag = True
# output this family id, the locus, the species with that locus, the genes on that locus,\
# the species tree branch on which the duplication occurred, and the daughter of the duplication node in the locus tree
if flag:
leaf_sps = []
leaf_gns = []
for gn, sp in lst:
if not gn.isdigit():
leaf_sps.append(sp)
leaf_gns.append(gn)
gnodes = [tree.nodes[name] for name in leaf_gns]
lca = treelib.lca(gnodes)
output.write('\t'.join([str(famid), locus, ','.join(leaf_sps), ','.join(leaf_gns), locus_sname[locus], lca.name]))
output.write('\n')
break
# if it is a true case, add to count
if flag:
count += 1
# print total count and close output file
print "Total number of true cases =", count
output.close()
#=============================================================================
# parse options
conf, args = o.parse_args()
#gene2species = phylo.read_gene2species(conf.smap)
stree = treelib1.read_tree(conf.stree)
tree = treelib1.read_tree(conf.tree)
if conf.names:
snames = dict(util.read_delim(conf.names))
else:
snames = None
if conf.brecon:
brecon = phylo.read_brecon(conf.brecon, tree, stree)
elif conf.recon:
recon, events = phylo.read_recon_events(conf.recon, tree, stree)
brecon = phylo.recon_events2brecon(recon, events)
else:
gene2species = phylo.read_gene2species(conf.smap)
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
brecon = phylo.recon_events2brecon(recon, events)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
transsvg.draw_tree(tree, brecon, stree, filename=conf.output, snames=snames)