def dummy(self, reftree, alignment):
seqs = SeqGroup(sequences=alignment, format='fasta')
entries = seqs.get_entries()
seq0 = entries[0][1]
dummyseq = seq0[:-50] + "A"*50
seqs.set_seq(name = "dummy", seq = dummyseq)
fout = self.tmppath + "/dummy" + self.name + ".fa"
seqs.write(format='fasta', outfile=fout)
self.run(reftree = reftree, alignment = fout)
self.clean()
os.remove(fout)
return self.tmppath + "/" + "RAxML_portableTree." + self.name + ".jplace"
def epa_2_ptp(epa_jp, ref_jp, full_alignment, min_lw = 0.5, debug = False):
placements = epa_jp.get_placement()
reftree = Tree(epa_jp.get_std_newick_tree())
allnodes = reftree.get_descendants()
species_list = []
placemap = {}
"""find how many edges are used for placement, and create a map to store """
for placement in placements:
edges = placement["p"]
curredge = edges[0][0]
lw = edges[0][2]
if lw >= min_lw:
placemap[curredge] = placemap.get(curredge, [])
"""group taxa name by placement branch"""
for placement in placements:
edges = placement["p"]
taxa_names = placement["n"]
curredge = edges[0][0]
lw = edges[0][2]
if lw >= min_lw:
a = placemap[curredge]
a.extend(taxa_names)
placemap[curredge] = a
groups = placemap.items()
cnt_leaf = 0
cnt_inode = 0
"""check each placement edge"""
for i,item in enumerate(groups):
place_branch_name = item[0]
seqset = item[1]
if len(seqset) < 4:
species_list.append(seqset)
else:
branch_alignment = SeqGroup()
for taxa in seqset:
branch_alignment.set_seq(taxa, full_alignment.get_seq(taxa))
species = build_tree_run_ptp(branch_alignment, ref_jp.get_rate())
species_list.extend(species)
return species_list
def get_ref_alignment(self):
entries = self.jdata["sequences"]
alignment = SeqGroup()
for entr in entries:
alignment.set_seq(entr[0], entr[1])
return alignment
