def phylomedump_tree_iterator( tarfn,verbose=0 ):
"""PhylomeDB all_trees.tar.gz dump treeobj generator."""
#open tarfile
if tarfn.endswith(".gz"):
tar = tarfile.open(tarfn, "r:gz")
else:
tar = tarfile.open(tarfn, "r")
i = k = 0
#process entries
for m in tar:
#if i>100: break
if not m.isfile():
continue
#load tree
if m.name.endswith(".nw"):
i += 1
#get nw
nw = tar.extractfile(m).readline()
t = PhyloTree(nw)
##add seedid and method info
#Phy000CWA9_YEAST.JTT.nw --> Phy000CWA9_YEAST JTT
seedid, method = os.path.basename(m.name).split(".")[:2]
t.seedid = seedid
t.method = method
#or add lk, seedid, method and lk to treeobj
elif m.name.endswith(".lk"):
seedid, method, lk = tar.extractfile(m).readline().split('\t')[:3]
t.lk = float(lk)
if not t.lk:
sys.stderr.write( " Err: Zero likelihood (%s) for: %s\n" % (t.lk, ", ".join((t.seedid, t.method))))
continue
if seedid!=t.seedid or t.method != method:
sys.stderr.write( " Err: Seedid and/or method doesn't match: %s\n" % ", ".join((seedid, t.seedid, method, t.method)))
continue
k += 1
if verbose and not i%100:
sys.stderr.write( " %6i\r" % i )
yield t
if verbose:
sys.stderr.write( " %s out of %s trees succesfully parsed [memory: %s KB]\n" % (k, i, resource.getrusage(resource.RUSAGE_SELF).ru_maxrss))
