def refine(query_fasta, start_fasta, deep_paralog_cutoff, num_cores):
gene_name = get_filename_from_path(query_fasta)[1].split(".")[0]
outdir, fasta = get_filename_from_path(start_fasta)
#print outdir,fasta
deep_paralog_cutoff = float(deep_paralog_cutoff)
query_ids = [s.name for s in seq.read_fasta_file(query_fasta)]
new_fasta = [] # list of output refined fasta files
print outdir, fasta
# make a tree from the start_fasta
tree = fasta_to_tree.fasta_to_tree(outdir, fasta, num_cores, "aa")
if tree == None: return []
with open(tree, "r") as infile:
intree = newick3.parse(infile.readline())
root = trim_tips.trim(intree,
relative_cutoff=deep_paralog_cutoff,
absolute_cutoff=deep_paralog_cutoff * 2)
if os.path.exists(outdir + fasta + ".pasta.aln-cln"):
clnfile = outdir + fasta + ".pasta.aln-cln"
else:
clnfile = outdir + fasta + ".mafft.aln-cln"
root = mask_tips_by_taxonID_transcripts.mask(root,\
clnfile=clnfile,\
para="y",
ignore=GENOMES)
if root != None:
with open(tree + ".tt.mm", "w") as outfile:
outfile.write(newick3.tostring(root) + "\n")
subtrees = cut_long_internal_branches.cut_long_internal_branches(
root, cutoff=deep_paralog_cutoff)
count = 0
base_name = fasta.split(".")[0]
seqDICT = {} # key is seqid, value is seq
for s in seq.read_fasta_file(start_fasta):
seqDICT[s.name] = s.seq
for tree in subtrees:
if tree == None: continue
label_set = set(tree_utils.get_front_labels(tree))
if len(label_set) > 4 and len(label_set & set(query_ids)) > 0:
count += 1
with open(outdir + base_name + "_" + str(count) + ".subtree",
"w") as outfile:
outfile.write(newick3.tostring(tree) + ";\n")
with open(outdir + base_name + "_" + str(count) + ".fa",
"w") as outfile:
for seqid in tree_utils.get_front_labels(tree):
try:
outfile.write(">" + seqid + "\n" + seqDICT[seqid] +
"\n")
except:
print seqid, "not found in fasta file"
new_fasta.append(outdir + base_name + "_" + str(count) + ".fa")
return new_fasta
def taxon_name_subst(original,table=sys.path[0]+"/reverse_taxon_table"):
DICT = {} # key is seq acronym, value is full taxon name, separated by tab
with open(table, "r") as infile:
for line in infile:
spls = line.strip().split("\t")
if len(spls) > 1:
DICT[spls[0].replace("|","_")] = spls[1]
with open(original,"r") as infile:
line = infile.readline()
is_fasta = True if line[0] == ">" else False
if is_fasta: # for fasta files
infile = open(original,"r")
outfile = open(original+".name","w")
for line in infile:
if line[0] == ">":
outfile.write('>'+get_long_id(line.strip()[1:],DICT)+"\n")
else: outfile.write(line)
infile.close()
outfile.close()
else: # tree file
with open(original,"r") as infile:
intree = newick3.parse(infile.readline())
for i in intree.leaves():
print i.label,
i.label = get_long_id(i.label,DICT)
print i.label
with open(original+".name","w") as outfile:
outfile.write(newick3.tostring(intree)+";\n")
def main(treDIR,
clnDIR,
para,
intree_file_ending=INTREE_FILE_ENDING,
ignore=GENOMES):
if treDIR[-1] != "/": treDIR += "/"
if clnDIR[-1] != "/": clnDIR += "/"
assert para == "y" or para == "n", "mask paraphyletic tips? (y/n)"
mask_para = True if para == "y" else False
filecount = 0
filematch = {} #key is clusterID, value is the .aln-cln file
for i in os.listdir(clnDIR):
if i.endswith(".aln-cln"):
clusterID = get_clusterID(i)
assert clusterID not in filematch, \
"The clusterID "+clusterID+" repeats in "+clnDIR
filematch[clusterID] = i
for i in os.listdir(treDIR):
if i.endswith(intree_file_ending):
with open(treDIR + i, "r") as infile:
intree = newick3.parse(infile.readline())
print i
clusterID = get_clusterID(i)
filecount += 1
curroot = mask(intree,
clnDIR + filematch[clusterID],
para=mask_para,
ignore=GENOMES)
with open(treDIR + i + ".mm", "w") as outfile:
outfile.write(newick3.tostring(curroot) + ";\n")
assert filecount > 0, \
"No file ends with "+intree_file_ending+" found in "+treDIR
def main(treDIR, clnDIR, para, intree_file_ending=INTREE_FILE_ENDING):
if treDIR[-1] != "/": treDIR += "/"
if clnDIR[-1] != "/": clnDIR += "/"
assert para == "y" or para == "n", "mask paraphyletic tips? (y/n)"
mask_para = True if para == "y" else False
filecount = 0
filematch = {} #key is clusterID, value is the .aln-cln file
for i in os.listdir(clnDIR):
if i.endswith(".aln-cln"):
clusterID = get_clusterID(i)
assert clusterID not in filematch, \
"The clusterID "+clusterID+" repeats in "+clnDIR
filematch[clusterID] = i
for i in os.listdir(treDIR):
if i.endswith(intree_file_ending):
with open(treDIR + i, "r") as infile:
intree = newick3.parse(infile.readline())
print i
clusterID = get_clusterID(i)
filecount += 1
chrDICT = {} #key is seqid, value is number of unambiguous chrs
for s in read_fasta_file(clnDIR + filematch[clusterID]):
for ch in ['-', 'X', "x", "?", "*"]:
s.seq = s.seq.replace(ch, "") #ignore gaps, xs and Xs
chrDICT[s.name] = len(s.seq)
curroot = mask_monophyletic_tips(intree, chrDICT)
if mask_para: curroot = mask_paraphyletic_tips(curroot, chrDICT)
with open(treDIR + i + ".mm", "w") as outfile:
outfile.write(newick3.tostring(curroot) + ";\n")
assert filecount > 0, \
"No file ends with "+intree_file_ending+" found in "+treDIR
def main(inDIR, file_ending, branch_len_cutoff, min_taxa, outDIR):
"""cut long branches and output subtrees as .subtre files
if uncut and nothing changed betwee .tre and .subtree
copy the original .tre file to the outdir"""
if inDIR[-1] != "/": inDIR += "/"
if outDIR[-1] != "/": outDIR += "/"
min_taxa = int(min_taxa)
filecount = 0
cutoff = float(branch_len_cutoff)
print "cutting branches longer than", cutoff
for i in os.listdir(inDIR):
if not i.endswith(file_ending): continue
print i
filecount += 1
with open(inDIR + i, "r") as infile: #only 1 tree in each file
intree = newick3.parse(infile.readline())
try:
with open(inDIR + i[:i.find(".tre")] + ".tre",
"r") as infile: #the original .tre
raw_tree_size = len(
get_front_labels(newick3.parse(infile.readline())))
except: # did not refine this round. Use the .tre.tt.mm tree
raw_tree_size = len(get_front_labels(intree))
num_taxa = count_taxa(intree)
if num_taxa < min_taxa:
print "Tree has", num_taxa, "less than", min_taxa, "taxa"
else:
print ".tre:", raw_tree_size, "tips; " + file_ending + ": " + str(
len(get_front_labels(intree))) + " tips"
subtrees = cut_long_internal_branches(intree, cutoff)
if len(subtrees) == 0:
print "No tree with at least", min_taxa, "taxa"
#elif raw_tree_size == len(subtrees[0].leaves()):
#copy(inDIR+i,outDIR+i)
#print "written to out directory unchanged"
else:
count = 0
outsizes = ""
for subtree in subtrees:
if count_taxa(subtree) >= min_taxa:
if subtree.nchildren == 2: #fix bifurcating roots from cutting
temp, subtree = remove_kink(subtree, subtree)
count += 1
with open(
outDIR + i.split(".")[0] + "_" + str(count) +
".subtree", "w") as outfile:
outfile.write(newick3.tostring(subtree) + ";\n")
outsizes += str(len(subtree.leaves())) + ", "
print count, "tree(s) wirtten. Sizes:", outsizes
assert filecount > 0, "No file end with " + file_ending + " in " + inDIR
def main(DIR, tree_file_ending, relative_cut, absolute_cut):
if DIR[-1] != "/": DIR += "/"
filecount = 0
for i in os.listdir(DIR):
if i.endswith(tree_file_ending):
print i
filecount += 1
with open(DIR + i, "r") as infile:
intree = newick3.parse(infile.readline())
outtree = trim(intree, float(relative_cut), float(absolute_cut))
if outtree != None:
with open(DIR + i + ".tt", "w") as outfile:
outfile.write(newick3.tostring(outtree) + ";\n")
assert filecount > 0, \
"No file end with "+tree_file_ending+" found in "+DIR
def main(DIR,tree_file_ending,relative_cut,absolute_cut1,absolute_cut2): if DIR[-1] != "/": DIR += "/" filecount = 0 for i in os.listdir(DIR): if i.endswith(tree_file_ending): print i filecount += 1 with open(DIR+i,"r") as infile: intree = newick3.parse(infile.readline()) outtree = trim(intree,float(relative_cut),float(absolute_cut1),float(absolute_cut2)) if outtree != None: with open(DIR+i+".tt","w") as outfile: outfile.write(newick3.tostring(outtree)+";\n") assert filecount > 0, \ "No file end with "+tree_file_ending+" found in "+DIR
import phylo3,newick3,os,sys
from tree_utils import *
if __name__ == "__main__":
if len(sys.argv) != 4:
print "python prune_paralogs_from_rooted_trees.py homoTreeDIR tree_file_ending minimal_taxa outDIR"
sys.exit(0)
inDIR = sys.argv[1]+"/"
tree_file_ending = sys.argv[2]
MIN_TAXA = int(sys.argv[3])
outDIR = sys.argv[4]+"/"
for i in os.listdir(inDIR):
if not i.endswith(tree_file_ending) continue
print i
outID = outDIR+get_clusterID(i)
with open(inDIR+i,"r") as infile:
intree = newick3.parse(infile.readline())
orthologs = get_ortho_from_rooted_inclade(intree)
count = 1
for ortho in orthologs:
if len(set(get_front_names(ortho))) >= MIN_TAXA:
with open(outID+".ortho"+str(count)+".tre","w") as outfile:
outstring = newick3.tostring(ortho)
#outstring = outstring.replace(":0",":1")
outfile.write(outstring+";\n")
count += 1
treDIR = sys.argv[1]+"/"
clnDIR = sys.argv[2]+"/"
outDIR = sys.argv[3]+"/"
if sys.argv[4] == "y": mask_para = True
elif sys.argv[4] == "n": mask_para = False
else:
print "mask_para? y/n"
sys.exit()
filecount = 0
for i in os.listdir(treDIR):
if i[-3:] == ".tt" and i[-3:] != ".mm":
with open(treDIR+i,"r") as infile:
intree = newick3.parse(infile.readline())
print i
clusterID = i.split("_")[0]
filecount += 1
unamb_chrDICT = {} #key is seqid, value is number of unambiguous chrs
with open(clnDIR+clusterID+ALIGNMENT_FILE_ENDING) as handle:
for record in SeqIO.parse(handle,"fasta"):
seqid,seq = str(record.id), str(record.seq)
for ch in ['-','X',"x","?","*"]:
seq = seq.replace(ch,"") #ignore gaps, xs and Xs
unamb_chrDICT[seqid] = len(seq)
curroot = monophyly_masking(intree,unamb_chrDICT)
if mask_para:
curroot = paraphyly_masking(curroot,unamb_chrDICT)
with open(outDIR+i+".mm","w") as outfile:
outfile.write(newick3.tostring(curroot)+";\n")
if filecount == 0:
print "No file name with 'best' or 'tt' or 'fasttree' found in the treDIR"
nc = n
while (not nc.istip) and len(nc.children) == 0:
print "pruning an empty tip"
np = nc.parent
nc.prune()
if np:
nc = np
else:
break
# if not n.istip:
# if len(n.children) == 0:
# nodes_to_remove.insert(0,n)
# else:
# empty = True
# for c in n.children:
# if c not in nodes_to_remove:
# empty = False
# break
# if empty:
# nodes_to_remove.insert(0,n)
#print ""
#for dud in nodes_to_remove:
# print "removing an empty tip!"
# dud.parent.remove_child(dud)
outfile = open(treefname.rsplit(".tre",1)[0] + ".renamed.tre","w")
outfile.write(newick3.tostring(tree) + ";")
outfile.close()
tip.prune()
# compress knuckle if there is one
# if len(parent.children) == 1:
# child = parent.children[0]
# if child.label != None:
# rightlabel = child.label
# else:
# rightlabel = ", ".join([leaf.label for leaf in child.leaves()])
# print "compressing a knuckle in the tree: " + leftlabel + " | " + rightlabel
# pp = parent.parent
# pp.remove_child(parent)
# pp.add_child(child)
#nodes_to_remove = []
for n in tree.descendants():
nc = n
while (not nc.istip) and len(nc.children) == 0:
print "pruning an empty tip"
np = nc.parent
nc.prune()
if np:
nc = np
else:
break
outfile = open(treefname.rsplit(".tre",1)[0] + ".pruned.tre","w")
outfile.write(newick3.tostring(tree) + ";")
outfile.close()
if seqid != "":
seqDICT[seqid] = seq
seqid,seq = line[1:].replace("-","_"),""
else: seq += line.strip()
seqDICT[seqid] = seq #add the last record
infile.close()
#cut by the first cutoff
print i,"Cutting branches longer than",cutoff1
outfile = open(DIR+ccID+".cut1.trees","w")
newtrees = [] #store trees in need of cutting for the next round
count = 0
while True:
for tree in trees:
if find_longest_internal_branch_length(tree) < cutoff1:
outfile.write(newick3.tostring(tree) +";\n")
#can be the original tree or cut tree. no need to cut tip here
else:
subtrees = cut_long_branches(tree,cutoff1)
for subtree in subtrees:
if count_ingroups(subtree) < MIN_INGROUP_TAXA: continue
count += 1
newname = DIR+ccID+".cut1-"+str(count)
with open(newname+".cutbranch","w") as outfile1: #record the cut branch
outfile1.write(newick3.tostring(subtree)+";\n")
with open(newname+".fa","w") as outfile2: #output fasta
for label in get_leaf_labels(subtree.leaves()):
outfile2.write(">"+label+"\n"+seqDICT[label]+"\n")
newaln = mafft_align(newname+".fa")
newcln = phyutility_clean_alignment(newaln)
newtreefile = fasttree(newcln)
#check taxonIDs ingroup_names = [] outgroup_names = [] for name in all_names: if name in INGROUPS: ingroup_names.append(name) elif name in OUTGROUPS: outgroup_names.append(name) else: print name,"not in ingroups or outgroups" sys.exit() if len(set(ingroup_names)) < MIN_INGROUP_TAXA: print "not enough ingroup taxa in tree" continue if len(outgroup_names) == 0: print "No outgroup in tree" continue inclades = extract_rooted_ingroup_clades(curroot,INGROUPS,OUTGROUPS,MIN_INGROUP_TAXA) inclade_count = 0 for inclade in inclades: inclade_count += 1 with open(outDIR+treefile+"."+str(inclade_count),"w") as outfile: outfile.write(newick3.tostring(inclade)+";\n") for node in inclade.iternodes(): if node.istip: node.label = get_name(node.label) # output multi-labeled tree for phyparts with open(phypartsDIR+treefile+"."+str(inclade_count),"w") as outfile: outfile.write(newick3.tostring(inclade)+";\n") print inclade_count,"clades extracted"
def mask_paraphyletic_tips(curroot,ignore=[]):
going = True
while going and curroot != None and len(curroot.leaves()) >= 4:
going = False
for node in curroot.iternodes(): #walk through nodes
if not node.istip: continue #only look at tips
name = get_name(node.label).split("_")[1]
parent = node.parent
if node == curroot or parent == curroot or parent == None:
continue #no paraphyletic tips for the root
for para in parent.get_sisters():
if para.istip and name==get_name(para.label).split("_")[1]: # mask
node = para.prune()
if len(curroot.leaves()) >= 4:
if (node==curroot and node.nchildren==2) or (node!=curroot and node.nchildren==1):
node,curroot = remove_kink(node,curroot)
going = True
break
return curroot
if __name__ == "__main__":
if len(sys.argv) != 3:
print "usage: python "+sys.argv[0]+" treefile para(y/n)"
sys.exit()
intree = newick3.parse(open(sys.argv[1],"r").readline())
masked = mask_monophyletic_tips(intree,ignore=[])
if sys.argv[2] == "y":
masked = mask_paraphyletic_tips(masked,ignore=[])
print newick3.tostring(masked)+";\n"
def RT(homoDIR, tree_file_eneding, outDIR, min_ingroup_taxa,
taxon_code_file_file):
if homoDIR[-1] != "/": homoDIR += "/"
if outDIR[-1] != "/": outDIR += "/"
min_ingroup_taxa = int(min_ingroup_taxa)
INGROUPS = []
OUTGROUPS = []
with open(taxon_code_file_file, "r") as infile:
for line in infile:
if len(line) < 3: continue
spls = line.strip().split("\t")
if spls[0] == "IN": INGROUPS.append(spls[1])
elif spls[0] == "OUT": OUTGROUPS.append(spls[1])
else:
print "Check taxon_code_file file format"
sys.exit()
if len(set(INGROUPS) & set(OUTGROUPS)) > 0:
print "Taxon ID", set(INGROUPS) & set(
OUTGROUPS), "in both ingroups and outgroups"
sys.exit(0)
print len(INGROUPS), "ingroup taxa and", len(
OUTGROUPS), "outgroup taxa read"
print "Ingroups:", INGROUPS
print "Outgroups:", OUTGROUPS
for treefile in os.listdir(homoDIR):
if not treefile.endswith(tree_file_eneding): continue
with open(homoDIR + treefile, "r") as infile:
intree = newick3.parse(infile.readline())
curroot = intree
all_names = tree_utils.get_front_names(curroot)
num_tips = len(all_names)
num_taxa = len(set(all_names))
print treefile
#check taxonIDs
ingroup_names = []
outgroup_names = []
for name in all_names:
if name in INGROUPS:
ingroup_names.append(name)
elif name in OUTGROUPS:
outgroup_names.append(name)
else:
print name, "not in ingroups or outgroups"
sys.exit()
if len(set(ingroup_names)) < min_ingroup_taxa:
print "not enough ingroup taxa in tree"
continue
outID = outDIR + tree_utils.get_clusterID(treefile)
if len(outgroup_names
) > 0: #at least one outgroup present, root and cut inclades
inclades = tree_utils.extract_rooted_ingroup_clades(curroot,\
INGROUPS,OUTGROUPS,min_ingroup_taxa)
inclade_count = 0
for inclade in inclades:
inclade_count += 1
inclade_name = outID + ".inclade" + str(inclade_count)
with open(inclade_name, "w") as outfile:
outfile.write(newick3.tostring(inclade) + ";\n")
orthologs = tree_utils.get_ortho_from_rooted_inclade(inclade)
ortho_count = 0
for ortho in orthologs:
if len(tree_utils.get_front_labels(
ortho)) >= min_ingroup_taxa:
ortho_count += 1
with open(
inclade_name + ".ortho" + str(ortho_count) +
".tre", "w") as outfile:
outfile.write(newick3.tostring(ortho) + ";\n")
elif len(all_names) == num_taxa:
#only output ortho tree when there is no taxon repeats
with open(outID + ".unrooted-ortho.tre", "w") as outfile:
outfile.write(newick3.tostring(curroot) + ";\n")
else: #do not attempt to infer direction of gene duplication without outgroup info
print "duplicated taxa in unrooted tree"
print "python trim_tips.py treDIR tree_file_ending outDIR relative_cutoff absolute_cutoff1 absolute_cutoff2"
sys.exit(0)
treDIR = sys.argv[1] + "/"
file_ending = sys.argv[2]
outDIR = sys.argv[3] + "/"
relative_cutoff = float(sys.argv[4])
absolute_cutoff1 = float(sys.argv[5])
absolute_cutoff2 = float(sys.argv[6])
done = [] #record clusterIDs that are done
for i in os.listdir(treDIR):
if i[-3:] == ".tt":
done.append(i.split(".")[0])
print done
filecount = 0
l = len(file_ending)
for i in os.listdir(treDIR):
if file_ending in i:
clusterID = i.split(".")[0]
if clusterID in done: continue
print i
filecount += 1
with open(treDIR + i, "r") as infile:
intree = newick3.parse(infile.readline())
with open(outDIR + i + ".tt", "w") as outfile:
outfile.write(newick3.tostring(cut_long_tips(intree)) + ";\n")
if filecount == 0:
print "No file name with", file_ending, "found in the treDIR"
if sister.istip and get_name(node.label)==get_name(sister.label): if node.length > sister.length: node = node.prune() else: node = sister.prune() if len(curroot.leaves()) >= 4: if node.nchildren==1 or (node==curroot and node.nchildren==2): node,curroot = remove_kink(node,curroot) #no kink if the original node had more than 2 children going = True break return curroot if __name__ == "__main__": if len(sys.argv) != 2: print "python mask_tips_by_taxonID_genomes.py DIR" sys.exit() DIR = sys.argv[1]+"/" filecount = 0 for i in os.listdir(DIR): if i[-3:] == ".tt": #only mask trees that have tips trimmed with open(DIR+i,"r") as infile: intree = newick3.parse(infile.readline()) print i filecount += 1 with open(DIR+i+".mm","w") as outfile: outfile.write(newick3.tostring(monophyly_masking_by_bl(intree))+";\n") if filecount == 0: print "No file name with 'best' or 'tt' or 'fasttree' found in the treDIR"
#check to make sure that the ingroup and outgroup names were set correctly for name in names: if name not in INGROUPS and name not in OUTGROUPS: print "check name",name sys.exit() outgroup_names = get_front_outgroup_names(curroot) #if no outgroup at all, do not attempt to resolve gene duplication if len(outgroup_names) == 0: print "duplicated taxa in unrooted tree" #skip the homolog if there are duplicated outgroup taxa elif len(outgroup_names) > len(set(outgroup_names)): print "outgroup contains taxon repeats" else: #at least one outgroup present and there's no outgroup duplication if curroot.nchildren == 2: #need to reroot temp,curroot = remove_kink(curroot,curroot) curroot = reroot_with_monophyletic_outgroups(curroot) #only return one tree after prunning if curroot != None: with open(outID+".reroot","w") as outfile: outfile.write(newick3.tostring(curroot)+";\n") ortho = prune_paralogs_from_rerooted_homotree(curroot) if len(set(get_front_names(curroot))) >= MIN_TAXA: with open(outID+".ortho.tre","w") as outfile: outfile.write(newick3.tostring(ortho)+";\n") else: print "not enough taxa after pruning" else: print "outgroup non-monophyletic"
filecount = 0
for i in os.listdir(inDIR):
if "best" not in i and i[-3:] != ".mm": continue
filecount += 1
if "best" in i:
clusterID = i.split(".")[1]
else: clusterID = i.split(".")[0]
print clusterID
with open(inDIR+i,"r") as infile: #only 1 tree in each file
intree = newick3.parse(infile.readline())
curroot = intree
if count_ingroup_taxa(curroot) < min_ingroup_taxa: continue
subtrees = cut_long_internal_branches(curroot,branch_len_cutoff)
if len(subtrees) > 0:
count = 1
for subtree in subtrees:
if count_ingroup_taxa(subtree)>=min_ingroup_taxa and count_outgroup_taxa(subtree)>=min_outgroup_taxa:
#fix bifurcating roots from cutting
if subtree.nchildren == 2:
subtree,subtree = remove_kink(subtree,subtree)
with open(outDIR+clusterID+"_subtree"+str(count)+".tre","w") as outfile:
outfile.write(newick3.tostring(subtree)+";\n")
count += 1
if filecount == 0:
print "No file end with",file_ending,"found"
print "python trim_tips.py treDIR tree_file_ending outDIR relative_cutoff absolute_cutoff1 absolute_cutoff2"
sys.exit(0)
treDIR = sys.argv[1]+"/"
file_ending = sys.argv[2]
outDIR = sys.argv[3]+"/"
relative_cutoff = float(sys.argv[4])
absolute_cutoff1 = float(sys.argv[5])
absolute_cutoff2 = float(sys.argv[6])
done = [] #record clusterIDs that are done
for i in os.listdir(treDIR):
if i[-3:] == ".tt":
done.append(i.split(".")[0])
print done
filecount = 0
l = len(file_ending)
for i in os.listdir(treDIR):
if file_ending in i:
clusterID = i.split(".")[0]
if clusterID in done: continue
print i
filecount += 1
with open(treDIR+i,"r") as infile:
intree = newick3.parse(infile.readline())
with open(outDIR+i+".tt","w") as outfile:
outfile.write(newick3.tostring(cut_long_tips(intree))+";\n")
if filecount == 0:
print "No file name with",file_ending,"found in the treDIR"