def run_anc(input_dict,run_id = None):
assert run_id
rank_name = input_dict['rank_name']
taxon_id = input_dict['taxid']
aliname = input_dict['aliname']
BT = getBTOL()
p_node = ncbi.get_node(taxon_id)
seqnodes = BT.investigatePhylum(p_node = p_node)
recs, seqelts, seqtuples = seq_recs(seqnodes)
align = align_seqnodes(recs)
tree = phyml.tree(align, run_id = run_id)
rstfile= paml.run_paml(tree, align, run_id = run_id)
anc_tree = paml.rst_parser(rstfile)
anc_alignment = [SeqRecord(elt.m['seq'],
id = None,
name = elt.name,
annotations = {'scores':elt.m['probs']})
for elt in anc_tree.get_nonterminals()]
out_dict = dict(anc_tree=anc_tree,
anc_align= anc_alignment,
term_tree = tree,
term_align = align)
return out_dict
def set_taxnodes(**kwargs):
all_seqs = get_seqs(dbname,**mem.sr(kwargs))
seq_taxa = [s.source_taxon
if s.source_taxon else None
for s in all_seqs]
alinodes = [ncbi.get_node(s) if s != None else None for s in seq_taxa]
return alinodes
def investigatePhylum(self,
aliname = 'group2.stk',
p_node = None, **kwargs):
if not p_node: p_node = ncbi.taxon_with_name('phylum', 'Thermotogae')
ali_seqs = ali.get_seqs(aliname, **mem.sr(kwargs))
ali_nodes = array(ali.get_taxnodes(aliname, **mem.sr(kwargs)))
ali_phyla = array(ali.get_taxon_forall(aliname,**mem.sr(kwargs, rank = 'phylum')))
ali_inds = nonzero(equal(ali_phyla, p_node))[0]
leaf_terminals = self.t.get_terminals()
leaf_nodes = array(self.leafNodes(**mem.sr(kwargs)))
leaf_phyla = array(self.getTaxon('phylum', **mem.sr(kwargs)))
leaf_inds = nonzero(equal(leaf_phyla, p_node))[0]
ap_sub = ali_phyla[ali_inds]
lp_sub = leaf_phyla[leaf_inds]
ag_sub = array(ali.get_taxon_forsome(ali_nodes[ali_inds],'genus','thermo',
**mem.sr(kwargs)))
lg_sub = array(self.getTaxon('genus', **mem.sr(kwargs)))[leaf_inds]
as_sub = array(ali.get_taxon_forsome(ali_nodes[ali_inds], 'species', 'thermo'))
ls_sub = array(self.getTaxon('species',**mem.sr(kwargs)))[leaf_inds]
db16 = cbdb.getName('16s')
a_16s= [ db16.S.q(db16.Sequence).
filter_by(source_taxon = n.id).all() for n in ali_nodes[ali_inds]]
l_16s= [ db16.S.q(db16.Sequence).
filter_by(source_taxon = n.id).all() for n in leaf_nodes[leaf_inds]]
#fill any empty nodes... (those lacking 16s rRNA)
for idx, elt in enumerate(a_16s):
cur_node= ali_nodes[ali_inds[idx]]
while not elt:
cur_node = cur_node.parent
elt.extend(db16.S.q(db16.Sequence).filter_by(source_taxon = cur_node.id).all())
for idx, elt in enumerate(l_16s):
cur_node= leaf_nodes[leaf_inds[idx]]
while not elt:
cur_node = cur_node.parent
elt.extend(db16.S.q(db16.Sequence).filter_by(source_taxon = cur_node.id).all())
all_lens = dict([ (k, [len(list( e)) for e in seqlist] )
for seqlist,k in [[a_16s,'a_16s'],[l_16s,'l_16s']]])
leaf_sns = [ SeqNode(lg_sub[i],ls_sub[i] , leaf_nodes[idx],
[(x.sequence,x.gb_id, x.source_taxon, ncbi.get_node(x.source_taxon).rank)
for x in l_16s[i]],
src = leaf_terminals[idx],
node_id = 'btol:default:{0}'.format(leaf_terminals[idx].m['id']))
for i, idx in enumerate(leaf_inds)]
ali_sns = [ SeqNode(ag_sub[i],as_sub[i] , ali_nodes[idx],
[( x.sequence,x.gb_id , x.source_taxon, ncbi.get_node(x.source_taxon).rank)
for x in a_16s[i]],
src = ali_seqs[idx],
node_id = 'ali:{0}:{1}'.format(aliname,ali_seqs[idx].id))
for i, idx in enumerate(ali_inds)]
return list(it.chain(leaf_sns, ali_sns))
def setLeafNodes(**kwargs):
all_leaves = self.t.get_terminals()
dbi = cbdb.getName('taxdmp')
all_nodes = [ ncbi.get_node(l.m['taxid'],dbi)
if 'taxid' in l.m.keys() else None for l in all_leaves]
return all_nodes