def main(inDIR, file_ending, branch_len_cutoff, min_taxa, outDIR, log):
"""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 += "/"
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 = tree_reader.read_tree_string(infile.readline())
try:
with open(inDIR + i[:i.find(".tre")] + ".tre",
"r") as infile: #the original .tre
raw_tree_size = len(
get_front_labels(
tree_reader.read_tree_string(infile.readline())))
except: # did not refine this round. Use the .tre.tt.mm tree
raw_tree_size = len(get_front_labels(intree))
num_taxa = len(intree.leaves())
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, min_taxa)
if len(subtrees) == 0:
print "No tree with at least", min_taxa, "taxa"
else:
count = 0
outsizes = ""
for subtree in subtrees:
if len(subtree.leaves()) >= min_taxa:
if len(subtree.children
) == 2: #fix bifurcating roots from cutting
temp, subtree = remove_kink(subtree, subtree)
count += 1
outname = outDIR + "/" + i.split(".")[0] + "_" + str(
count) + ".subtree"
print outname
with open(outname, "w") as outfile:
outfile.write(
subtree.get_newick_repr(True) + ";\n")
outsizes += str(len(subtree.leaves())) + ", "
print count, "tree(s) written. Sizes:", outsizes
def main(treefile, relative_cut, absolute_cut):
intree = None
with open(treefile, "r") as infile:
intree = tree_reader.read_tree_string(infile.readline())
outtree, removed = trim(intree, float(relative_cut), float(absolute_cut))
print outtree.get_newick_repr(True) + ";"
return outtree, removed
def load_one_study(studyloc,study_treeid,javapre,treemloc,dload,outfile,treeoutfile,append):
load_nexson(studyloc,study_treeid,javapre,treemloc,dload,outfile,append)
source_explorer(study_treeid,javapre,treemloc,dload,treeoutfile,append)
#attempt to read the tree
tf = open(treeoutfile,"r")
tree = read_tree_string(tf.readline())
print "root name:"+tree.label
tf.close()
def load_one_study_inf_mono(studyloc,study_treeid,javapre,treemloc,dload,outfile,treeoutfile,infmonofile,append):
load_nexson(studyloc,study_treeid,javapre,treemloc,dload,outfile,append)
source_explorer(study_treeid,javapre,treemloc,dload,treeoutfile,append)
tf = open(treeoutfile,"r")
tree = read_tree_string(tf.readline())
print "root name:"+tree.label
tf.close()
mapcompat_one_study(studyloc,study_treeid,javapre,treemloc,dload,outfile,outfile,True)
source_explorer_inf_mono(study_treeid,javapre,treemloc,dload,infmonofile,append)
def read_tree(in_tree,nwk=False):
if nwk == False:
nwk = open(in_tree,"r").readlines()[0].strip()
else:
nwk = in_tree
tree = tree_reader.read_tree_string(nwk)
for i in tree.iternodes():
i.old_length = i.length
return tree
def load_one_study_inf_mono(studyloc,study_treeid,javapre,treemloc,dload,outfile,treeoutfile,infmonofile,append):
load_nexson(studyloc,study_treeid,javapre,treemloc,dload,outfile,append)
studyid = "_".join(study_treeid.split("_")[:-1])
sha = get_git_SHA_from_json(studyloc+"/"+studyid)
source_explorer(study_treeid+"_"+sha,javapre,treemloc,dload,treeoutfile,append)
tf = open(treeoutfile,"r")
tree = read_tree_string(tf.readline())
print "root name:"+tree.label
tf.close()
mapcompat_one_study(studyloc,study_treeid,javapre,treemloc,dload,outfile,outfile,True)
source_explorer_inf_mono(study_treeid+"_"+sha,javapre,treemloc,dload,infmonofile,append)
def load_one_study(studyloc, study_treeid, javapre, treemloc, dload, outfile,
treeoutfile, append):
load_nexson(studyloc, study_treeid, javapre, treemloc, dload, outfile,
append)
sha = get_git_SHA(studyloc)
source_explorer(study_treeid + "_" + sha, javapre, treemloc, dload,
treeoutfile, append)
#attempt to read the tree
tf = open(treeoutfile, "r")
tree = read_tree_string(tf.readline())
print "root name:" + tree.label
tf.close()
def load_one_study_newick(treeid,javapre,treemloc,dload,outfile,treeoutfile,append):
load_newick(treeid,javapre,treemloc,dload,outfile,append)
studyid = treeid
print studyid
source_explorer(treeid,javapre,treemloc,dload,treeoutfile,append)
#attempt to read the tree
tf = open(treeoutfile,"r")
ts = None
for i in tf:
ts = i
tree = read_tree_string(ts)
print "root name:"+tree.label
tf.close()
return treeid
def load_one_study_inf_mono(studyloc, study_treeid, javapre, treemloc, dload,
outfile, treeoutfile, infmonofile, append):
load_nexson(studyloc, study_treeid, javapre, treemloc, dload, outfile,
append)
source_explorer(study_treeid, javapre, treemloc, dload, treeoutfile,
append)
tf = open(treeoutfile, "r")
tree = read_tree_string(tf.readline())
print "root name:" + tree.label
tf.close()
mapcompat_one_study(studyloc, study_treeid, javapre, treemloc, dload,
outfile, outfile, True)
source_explorer_inf_mono(study_treeid, javapre, treemloc, dload,
infmonofile, append)
def load_one_study(studyloc,study_treeid,javapre,treemloc,dload,outfile,treeoutfile,append):
load_nexson(studyloc,study_treeid,javapre,treemloc,dload,outfile,append)
studyid = "_".join(study_treeid.split("_")[:-1])
print studyid
sha = get_git_SHA_from_json(studyloc+"/"+studyid)
source_explorer(study_treeid+"_"+sha,javapre,treemloc,dload,treeoutfile,append)
#attempt to read the tree
tf = open(treeoutfile,"r")
ts = None
for i in tf:
ts = i
tree = read_tree_string(ts)
print "root name:"+tree.label
tf.close()
return sha
def load_one_study_newick(treeid, javapre, treemloc, dload, outfile,
treeoutfile, append):
load_newick(treeid, javapre, treemloc, dload, outfile, append)
studyid = treeid
print studyid
source_explorer(treeid, javapre, treemloc, dload, treeoutfile, append)
#attempt to read the tree
tf = open(treeoutfile, "r")
ts = None
for i in tf:
ts = i
tree = read_tree_string(ts)
print "root name:" + tree.label
tf.close()
return treeid
def load_one_study(studyloc, study_treeid, javapre, treemloc, dload, outfile,
treeoutfile, append):
load_nexson(studyloc, study_treeid, javapre, treemloc, dload, outfile,
append)
studyid = "_".join(study_treeid.split("_")[:-1])
print studyid
sha = get_git_SHA_from_json(studyloc + "/" + studyid)
source_explorer(study_treeid + "_" + sha, javapre, treemloc, dload,
treeoutfile, append)
#attempt to read the tree
tf = open(treeoutfile, "r")
ts = None
for i in tf:
ts = i
tree = read_tree_string(ts)
print "root name:" + tree.label
tf.close()
return sha
def load_one_study_inf_mono(studyloc, study_treeid, javapre, treemloc, dload,
outfile, treeoutfile, infmonofile, append):
load_nexson(studyloc, study_treeid, javapre, treemloc, dload, outfile,
append)
studyid = "_".join(study_treeid.split("_")[:-1])
sha = get_git_SHA_from_json(studyloc + "/" + studyid)
source_explorer(study_treeid + "_" + sha, javapre, treemloc, dload,
treeoutfile, append)
tf = open(treeoutfile, "r")
ts = tf.readline()
# ignore output that isn't a tree
while ts[0] != '(':
ts = tf.readline()
tree = read_tree_string(ts)
print "root name:" + tree.label
tf.close()
mapcompat_one_study(studyloc, study_treeid, javapre, treemloc, dload,
outfile, outfile, True)
source_explorer_inf_mono(study_treeid + "_" + sha, javapre, treemloc,
dload, infmonofile, append)
dest='phyx_location',
default="",
help="where are pxlstr (and pxrmt if you have outgroups)")
par.add_argument('--outf', dest='outf', help="the outfile")
args = par.parse_args()
#parse the arguments
if args.fileending != None:
flend = args.fileending
di = args.di[0]
print "directory:", di
print "file ending for trees:", flend
spt = args.speciestree[0]
print "species tree:", spt
st = open(spt, "r")
tree = tree_reader.read_tree_string(st.readline())
st.close()
clades = get_clades(tree)
print "phyx location:", args.phyx_location
if args.phyx_location != "":
cmd = args.phyx_location + "/" + cmd
if args.outf != None:
print "outfile:", args.outf
writetofile = True
outf = open(args.outf, 'w')
for i in os.listdir(di):
if i[-len(flend):] == flend:
fd = di + "/" + i
p = subprocess.Popen(cmd + fd, shell=True, stdout=subprocess.PIPE)
x = p.communicate()[0].split("\n")
pp = parent.parent
ch = parent.children[0]
pp.remove_child(parent)
parent.remove_child(ch)
pp.add_child(ch)
ch.parent = pp
break
else:
parent = parent.parent
if found == False:
going = False
break
return tree
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python " + sys.argv[0] + " infile.tre outfile.tre"
sys.exit()
infile = open(sys.argv[1], "r")
outfile = open(sys.argv[2], "w")
tree = tree_reader.read_tree_string(infile.readline())
infile.close()
tree = del_knees(tree)
if len(tree.children) == 1:
print "one child at root"
tree = tree.children[0]
outfile.write(tree.get_newick_repr() + ";")
outfile.close()
elif len(name) > 4 and name[-4:] == "ales":
return "order"
elif len(name) > 3 and name[-3:] == "eae":
return "tribe"
else:
return "genus"
return rank
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python " + sys.argv[0] + " infile.tre outfile.taxa"
sys.exit(0)
infile = open(sys.argv[1], "r")
stri = infile.readline()
tree = tree_reader.read_tree_string(stri)
infile.close()
names = {} #key is name, value is parent
nums = {} #key is name, value is number
cnum = 1
for i in tree.iternodes():
if len(i.label) > 0:
nums[i.label] = cnum
cnum += 1
if i.parent != None:
names[i.label] = i.parent.label
outfile = open(sys.argv[2], "w")
for i in nums:
#print i
p = ""
if i in names:
directory = "files_for_submission_v2.0/Inf-mono_log/"
tend = ".tre"
lend = ".log"
outfilen = "all.numtips.results"
if __name__ == "__main__":
studies = []
outfile = open(outfilen,"w")
for i in os.listdir(directory):
if lend in i:
studies.append(i[0:len(i)-len(lend)])
sl = set(studies)
for i in sl:
try:
fl = open(directory+"/"+i+tend,"r")
ts = fl.readline()
if "WARN" in ts:
ts = fl.readline()
fl.close()
if len(ts) > 1:
#read the tree first
tr = tree_reader.read_tree_string(ts)
outfile.write(str(len(list(tr.leaves())))+"\n")
except:
print "some problem with "+i
outfile.close()
directory = "files_for_submission_v2.0/Inf-mono_log/"
tend = ".tre"
lend = ".log"
outfilen = "all.numtips.results"
if __name__ == "__main__":
studies = []
outfile = open(outfilen, "w")
for i in os.listdir(directory):
if lend in i:
studies.append(i[0:len(i) - len(lend)])
sl = set(studies)
for i in sl:
try:
fl = open(directory + "/" + i + tend, "r")
ts = fl.readline()
if "WARN" in ts:
ts = fl.readline()
fl.close()
if len(ts) > 1:
#read the tree first
tr = tree_reader.read_tree_string(ts)
outfile.write(str(len(list(tr.leaves()))) + "\n")
except:
print "some problem with " + i
outfile.close()
sys.exit() from stephen_laptop_conf import * infile = sys.argv[1] outfile = sys.argv[2] temp1 = "tempfile1" temp2 = "tempfile2" cmd1 = "cp "+infile+" "+temp1 #copy to a temp os.system(cmd1) cmd2 = javapre +" "+treemloc+" checktaxhier "+ temp1 +" "+dott+" > "+temp2 #tax hier os.system(cmd2) #delete knees inf = open(temp2,"r") inf.readline() tree = tree_reader.read_tree_string(inf.readline().strip()+";") inf.close() tree = delete_knees.del_knees(tree) ouf = open(temp1,"w") ouf.write(tree.get_newick_repr()+";") ouf.close() #tax hier os.system(cmd2) #delete knees again inf = open(temp2,"r") inf.readline() tree = tree_reader.read_tree_string(inf.readline().strip()+";") inf.close() tree = delete_knees.del_knees(tree) ouf = open(outfile,"w") ouf.write(tree.get_newick_repr()+";")
import tree_reader
import sys
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python " + sys.argv[0] + " treefile namesfile"
sys.exit(0)
treefile = open(sys.argv[1], "r")
tfl = tree_reader.read_tree_string(treefile.readline())
lvsd = {}
for i in tfl.leaves():
lvsd[i.label] = i
treefile.close()
namesfile = open(sys.argv[2], "r")
names = []
namesd = {}
for i in namesfile:
nm = "ott" + i.strip().split(" ")[-1]
names.append(nm)
namesd[nm] = "_".join(i.strip().split(" ")[0:-1])
namesfile.close()
for i in names:
if i in lvsd:
lvsd[i].data["paint"] = True
cur = lvsd[i]
while cur != tfl:
cur = cur.parent
if "paint" in cur.data:
break
return "family"
elif len(name) > 4 and name[-4:] == "ales":
return "order"
elif len(name) > 3 and name[-3:] == "eae":
return "tribe"
else:
return "genus"
return rank
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python "+sys.argv[0]+" infile.tre outfile.taxa"
sys.exit(0)
infile = open(sys.argv[1],"r")
stri = infile.readline()
tree = tree_reader.read_tree_string(stri)
infile.close()
names = {} #key is name, value is parent
nums = {} #key is name, value is number
cnum = 1
for i in tree.iternodes():
if len(i.label) > 0:
nums[i.label] = cnum
cnum += 1
if i.parent != None:
names[i.label] = i.parent.label
outfile = open(sys.argv[2],"w")
for i in nums:
#print i
p = ""
if i in names:
found = True
pp = parent.parent
ch = parent.children[0]
pp.remove_child(parent)
parent.remove_child(ch)
pp.add_child(ch)
ch.parent = pp
break
else:
parent = parent.parent
if found == False:
going = False
break
return tree
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python "+sys.argv[0]+" infile.tre outfile.tre"
sys.exit()
infile = open(sys.argv[1],"r")
outfile = open(sys.argv[2],"w")
tree = tree_reader.read_tree_string(infile.readline())
infile.close()
tree = del_knees(tree)
if len(tree.children) == 1:
print "one child at root"
tree = tree.children[0]
outfile.write(tree.get_newick_repr()+";")
outfile.close()
treestring = ""
start = False
for i in fl:
if i.strip() == "MRP":
break
if start:
fl2.write(i)
treestring = i.strip()
break
if i.strip() == "TREEUID":
start = True
fl2.close()
fl.close()
print treestring
treestrings.append(treestring)
tree = tree_reader.read_tree_string(treestring)
for i in tree.leaves():
taxalist.add(i.label)
general_tm_utils.extract_taxonomy_from_ids(javapre,treemloc,dload,",".join(taxalist),taxtreefile)
outfile = open(mlsout,"w")
outfile.write("#NEXUS\n")
outfile.write("BEGIN TAXA;\n\tDIMENSIONS NTAX=");
ttf = open(taxtreefile,"r")
taxstring = ttf.readline()
tree = tree_reader.read_tree_string(taxstring);
taxs = []
for i in tree.iternodes():
taxs.append(i.label)
ttf.close()
outfile.write(str(len(taxs))+";\n\ttaxlabels\n")
for i in taxs:
type=str,
help='If provided, write species stats to this location (CSV)')
args = parser.parse_args()
# Read in data
pam = Matrix.load(args.pam_matrix_filename)
# We use a hack function to get the data out of the tree, in the LM code
# this is done with dendropy. I just didn't want to add any dependencies
tree_newick, squid_dict = munge_lm_tree(args.tree_filename)
#print tree_newick
#print len(squid_dict.keys())
# Read the newick tree
tree = read_tree_string(tree_newick)
# Generate stats matrices
site_stats = get_site_statistics(tree, pam, squid_dict)
species_stats = get_species_statistics(tree, pam, squid_dict)
# Write matrices if desired
if args.sites_filename is not None:
with open(args.sites_filename, 'w') as outF:
site_stats.writeCSV(outF)
else:
print site_stats.data
if args.species_filename is not None:
raise Exception, 'No species stats are currently implemented'
def run_bp_window(infn, tsegfiles, mltr, segc, outf):
write_r()
mlto = tree_reader.read_tree_file_iter(mltr).__next__()
mlbps = get_biparts(mlto)
segs = {}
segslong = {}
segstree = {}
plotsegs = [] # each row is a seg, each column is a node
conflictsegscount = []
count = 0
for i in range(len(tsegfiles)):
conflictcount = 0
segs[count] = []
segslong[count] = set()
plotsegs.append([0] * len(mlbps))
cmd = "bp -c " + mltr + " -t " + tsegfiles[i] + " -tv"
segstree[count] = open(tsegfiles[i], "r").readline()
o = subprocess.check_output(cmd.split(" "), stderr=subprocess.STDOUT)
keepo = str(o).split("\\n")
cf = keepo[-8]
cc = keepo[-7]
cft = tree_reader.read_tree_string(cf)
cct = tree_reader.read_tree_string(cc)
for j, k in zip(cft.iternodes(), cct.iternodes()):
if len(j.children) > 1:
sbp = None
inde = None
if j.label != "" or k.label != "":
sbp = get_bipart(j, cft)
inde = get_bp_ind(mlbps, sbp)
# conflict one
if j.label != "":
if int(j.label) > 0:
conflictcount += 1
segs[count].append(sbp)
plotsegs[i][inde] = -1
# process the bp out from above to record the actual split that conflicts
start = False
for l in keepo:
if start:
if " (" == l[0:3]:
tttt = tree_reader.read_tree_string(
l.strip().split(" ")[-1])
segslong[count] = add_bp(
segslong[count],
get_biparts(tttt)[0])
if "read " == l[0:5]:
start = True
if "TREES " == l[0:6]:
break
# concordant one
if k.label != "":
if int(k.label) > 0:
plotsegs[i][inde] = 1
if remove_intermediate_files:
otf = tsegfiles[i]
if os.path.exists(otf):
os.remove(otf)
conflictsegscount.append(
conflictcount) #just a running tally of the conflicts per segment
count += 1
# print the number of conflicts per segment
print(infn + " " + " ".join([str(k) for k in conflictsegscount]))
# print the verbose stuff to the gzip
detfile = gzip.open(outf + ".details.gz", "wt")
for i, sc, sl, t in zip(segs, segc, segslong, segstree):
detfile.write(
str(i) + " " + "-".join([str(k) for k in list(sc)]) + "\n")
for j in segs[i]:
detfile.write(" conflicts with:" + str(j) + "\n")
for j in segslong[i]:
detfile.write(" prefers:" + str(j) + "\n")
detfile.write(" tree:" + segstree[t] + "\n")
detfile.close()
# write the plotting information
ouf = open(outf, "w")
first = True
for sc in segc:
if first == True:
first = False
else:
ouf.write(" ")
ouf.write("\"" + "-".join([str(k) for k in list(sc)]) + "\"")
ouf.write("\n")
for i in range(len(mlbps)):
s = []
for j in range(len(plotsegs)):
s.append(str(plotsegs[j][i]))
ouf.write(" ".join(s) + "\n")
ouf.close()
cmd = "Rscript rplot.r " + outf + " " + outf + ".png " + infn[
0:min(15, len(infn))] + " > rlog 2>&1"
os.system(cmd)
species = species.replace(" ", "_")
# print(species)
woody_species.append(species)
print("Species with trait data: %d" %len(woody_species))
# Get tip names from tree
# Big tree
y = open("ALLOTB_binary_Names.tre", "r")
# Genbank data tree
# y = open("GBOTB.tre", "r")
y.seek(0)
# With Stephen's Tree_Reader
tree = tree_reader.read_tree_string(y.readline().strip())
tips = tree.lvsnms()
print("Tips in the tree: %d" %len(tips))
# With BioPython
# tree2 = Phylo.read("GBOTB.tre", "newick")
# tree2.count_terminals()
# tips2 = tree2.get_terminals()
# len(tips2)
# Find Intersect
species_intersect = list(set(woody_species) & set(tips))
percent_tips_with_traits = (len(species_intersect) * 100) / len(tips)
print("Species in the tree with trait data: %d (%.2f%%)" %(len(species_intersect), percent_tips_with_traits))
treestring = ""
start = False
for i in fl:
if i.strip() == "MRP":
break
if start:
fl2.write(i)
treestring = i.strip()
break
if i.strip() == "TREEUID":
start = True
fl2.close()
fl.close()
print treestring
treestrings.append(treestring)
tree = tree_reader.read_tree_string(treestring)
for i in tree.leaves():
taxalist.add(i.label)
general_tm_utils.extract_taxonomy_from_ids(javapre,treemloc,dload,",".join(taxalist),taxtreefile)
outfile = open(mlsout,"w")
outfile.write("#NEXUS\n")
outfile.write("BEGIN TAXA;\n\tDIMENSIONS NTAX=");
ttf = open(taxtreefile,"r")
taxstring = ttf.readline()
tree = tree_reader.read_tree_string(taxstring);
taxs = []
for i in tree.iternodes():
taxs.append(i.label)
ttf.close()
outfile.write(str(len(taxs))+";\n\ttaxlabels\n")
for i in taxs:
j.length = brlen
break
if match is False:
return False
if match is True:
return True
if __name__ == "__main__":
if len(sys.argv[1:]) == 0:
sys.argv.append("-h")
parser = argparse.ArgumentParser()
parser.add_argument("tree1", help="nwk tree to transfer brlen from")
parser.add_argument("tree2", help="nwk tree to transfer brlen to")
args = parser.parse_args()
with open(args.tree1, "r") as inf:
s = inf.readlines()[0].strip()
tree1 = tree_reader.read_tree_string(s)
with open(args.tree2, "r") as inf:
s = inf.readlines()[0].strip()
tree2 = tree_reader.read_tree_string(s)
if not transfer_brlen(tree1, tree2):
print("topologies are not identical!")
sys.exit()
else:
print(tree2.get_newick_repr(True))
import sys
import tree_reader
if __name__ == "__main__":
if len(sys.argv) != 2:
print "python " + sys.argv[0] + " infile.tre"
sys.exit(0)
inf = open(sys.argv[1], "r")
oneline = inf.readline().strip()
tree = tree_reader.read_tree_string(oneline)
for i in tree.iternodes():
if len(i.children) > 0:
i.label = i.note
inf.close()
print tree.get_newick_repr(True) + ";"
if "nodes" not in i.data:
i.data["nodes"] = set()
i.data["nodes"].add(j)
print i.get_newick_repr(False),j,nodesetslf[j],nodesetsrt[j]
if match == False:
print "NO MATCH for tree node: "+i.get_newick_repr(False)
if __name__ == "__main__":
if len(sys.argv) != 2:
print "python "+sys.argv[0]+" infile.tre"
sys.exit(0)
trees = []
infile = open(sys.argv[1],"r")
for i in infile:
trees.append(tree_reader.read_tree_string(i))
infile.close()
bipartslf = []
bipartsrt = []
#this generates the bipartions from the tree
for i in trees:
root = set(i.lvsnms())
for j in i.iternodes():
if len(j.children) > 0:# and i != j:
lvs = j.lvsnms()
lft = set(lvs)
rt = root - lft
bipartslf.append(lft)
bipartsrt.append(rt)
#these are the bipartitoins that are added as a result of summing like ab|e and ac|e -> abc|e
addlf = []#added as a result of equivalent
help="if robust. Tab-separated file \
of site, node, state, and probability, in the style \
of FastML's Ancestral_MaxMarginalProb_Char_Indel.txt")
args = parser.parse_args()
if args.robust and args.probs is None:
sys.stderr.write("must specify probability file (-p) to calculate " +
"robust substitutions\n")
sys.exit()
with open(args.tree, "r") as t:
for s in t:
s = s.strip()
nwkString = s
curroot = tree_reader.read_tree_string(nwkString)
branches = get_anc_desc(curroot)
seqs = dict([x for x in parse_fasta(args.sequences)])
# print(seqs)
if args.robust:
probs = parse_probs(args.probs)
add_subs_robust(branches, seqs, probs, args.gaps)
else:
add_subs(branches, seqs, args.gaps)
print("parent\tchild\tsubs")
print(curroot.label)
for k, v in branches.items():
print(k[0] + "\t" + k[1] + "\t" + ",".join(v))
else:
maxlen = max([ lf.length_to_root for lf in leaves ])
scalef = (leaves[0].c + 1 - root_offset)/maxlen
scale_cpos(tree, scalef, root_offset)
for node in tree.iternodes(order="postorder"):
if node.parent:
for r in range(min([node.r, node.parent.r]),
max([node.r, node.parent.r])):
buf.putstr(r, node.parent.c, ":")
sym = getattr(node, "hchar", "-")
vbar = sym*(node.c-node.parent.c)
buf.putstr(node.r, node.parent.c, vbar)
if node.istip:
buf.putstr(node.r, node.c+1, " "+node.label)
else:
if node.label and show_internal_labels:
buf.putstr(node.r, node.c-len(node.label), node.label)
buf.putstr(node.r, node.c, "+")
return str(buf)
if __name__ == "__main__":
import random
rand = random.Random()
t = tree_reader.read_tree_string("(foo,((bar,(dog,cat)),(shoe,(fly,(cow, bowwow)))));")
print tree2ascii(t, scaled=0, show_internal_labels=1)
