def calculate_region(arg):
prot, start, win, nseqs, trop_dict = arg
fname = 'phyliptrees/%s-%i-%i.tree' % (prot, start, win)
if os.path.exists(fname):
contree = dendropy.Tree.get_from_path(fname, 'nexus')
treeset = dendropy.TreeList.get_from_path(fname + 'set', 'nexus')
else:
alphabet = generic_protein if prot != 'LTR' else generic_dna
contree = TreeingTools.phylip_tree(nseqs, alphabet=alphabet)
treeset = dendropy.TreeList([contree])
contree.write_to_path(fname, 'nexus')
treeset.write_to_path(fname + 'set', 'nexus')
try:
bats_res = TreeingTools.run_bats(treeset, trop_dict, nreps = 1000)
except:
bats_res = None
try:
dmat = TreeingTools.get_pairwise_distances(contree)
benj_res = TreeingTools.check_distance_pvals(dmat, trop_dict, nreps = 50)
except:
benj_res = None
return prot, win, start, bats_res, benj_res
