/// Do a SPR move on T1, moving the subtree behind b1_ to branch b2
double do_SPR(SequenceTree& T1, int b1_,int b2)
{
const_branchview b1 = T1.directed_branch(b1_);
SequenceTree T2 = T1;
//------ Generate the new topology ------//
if (T2.directed_branch(b2).target() == b1.target() or
T2.directed_branch(b2).source() == b1.target())
;
else
SPR(T2,b1.reverse(),b2);
//------ Find the two new branches ------//
vector<const_branchview> connected1;
append(T1.directed_branch(b1.source(),b1.target()).branches_after(),connected1);
vector<const_branchview> connected2;
append(T2.directed_branch(b1.source(),b1.target()).branches_after(),connected2);
assert(connected1.size() == 2);
assert(connected2.size() == 2);
//------- Place the split randomly -------//
double L1 = connected1[0].length() + connected1[1].length();
double L2 = connected2[0].length() + connected2[1].length();
T2.directed_branch(connected2[0]).set_length( myrandomf() * L2 );
T2.directed_branch(connected2[1]).set_length( L2 - T2.directed_branch(connected2[0]).length() );
T1 = T2;
return L2/L1;
}
int choose_SPR_target(SequenceTree& T1, int b1_)
{
const_branchview b1 = T1.directed_branch(b1_);
//----- Select the branch to move to ------//
dynamic_bitset<> subtree_nodes = T1.partition(b1.reverse());
subtree_nodes[b1.target()] = true;
vector<int> branches;
vector<double> lengths;
for(int i=0; i<T1.n_branches(); i++)
{
const_branchview bi = T1.branch(i);
// skip branch if its contained in the subtree
if (subtree_nodes[bi.target()] and
subtree_nodes[bi.source()])
continue;
double L = 1.0;
// down-weight branch if it is one of the subtree's 2 neighbors
if (subtree_nodes[bi.target()] or
subtree_nodes[bi.source()])
L = 0.5;
branches.push_back(i);
lengths.push_back(L);
}
int b2 = branches[ choose(lengths) ];
return b2;
}
bool update_lengths(const SequenceTree& Q,const SequenceTree& T,
valarray<double>& branch_lengths,
valarray<double>& branch_lengths_squared,
valarray<double>& node_lengths)
{
// map branches from Q -> T
vector<int> branches_map = extends_map(T,Q);
if (not branches_map.size())
return false;
// incorporate lengths of branches that map to Q
for(int b=0;b<Q.n_branches();b++)
{
int b2 = branches_map[b];
double L = T.directed_branch(b2).length();
branch_lengths[b] += L;
branch_lengths_squared[b] += L*L;
}
// map nodes from T -> Q
vector<int> nodes_map = get_nodes_map(Q,T,branches_map);
// incorprate lengths of branches that map to nodes in Q
for(int i=T.n_leafbranches();i<T.n_branches();i++)
{
const_branchview b = T.branch(i);
int n1 = nodes_map[b.source()];
int n2 = nodes_map[b.target()];
if (n1 == n2)
node_lengths[n1] += T.branch(i).length();
}
return true;
}
B n_mutations(const alphabet& a, const vector<int>& letters, const SequenceTree& T,const ublas::matrix<B>& cost,
ublas::matrix<B>& n_muts, const vector<const_branchview>& branches)
{
int root = T.directed_branch(0).target();
peel_n_mutations(a,letters,T,cost,n_muts,branches);
return row_min(n_muts,root);
}
B n_mutations(const alphabet& a, const vector<int>& letters, const SequenceTree& T,const ublas::matrix<B>& cost)
{
int root = T.directed_branch(0).target();
vector<const_branchview> branches = branches_toward_node(T,root);
ublas::matrix<B> n_muts(T.n_nodes(), a.size());
return n_mutations(a,letters,T,cost,n_muts,branches);
}
vector<vector<int> > get_all_parsimony_letters(const alphabet& a, const vector<int>& letters, const SequenceTree& T,
const ublas::matrix<int>& cost)
{
int root = T.directed_branch(0).target();
ublas::matrix<int> n_muts(T.n_nodes(), a.size());
peel_n_mutations(a,letters,T,cost,n_muts, branches_toward_node(T,root) );
// get an order list of branches point away from the root;
vector<const_branchview> branches = branches_from_node(T,root);
std::reverse(branches.begin(),branches.end());
// Allocate space to store the letters for each node
vector<vector<int> > node_letters(T.n_nodes());
const unsigned A = a.size();
// choose the cheapest letters at the root
{
double m = row_min(n_muts,root);
for(int l=0;l<A;l++)
if (n_muts(root,l) <= m)
node_letters[root].push_back(l);
}
vector<double> temp(A);
for(int i=0;i<branches.size();i++)
{
int s = branches[i].source();
int t = branches[i].target();
vector<double> best(node_letters[s].size());
for(int j=0;j<node_letters[s].size();j++)
{
for(int l=0;l<A;l++)
temp[l] = n_muts(t,l)+cost(l,node_letters[s][j]);
best[j] = min(temp);
}
for(int l=0;l<A;l++)
{
bool is_best = false;
for(int j=0;j<node_letters[s].size() and not is_best;j++)
if (n_muts(t,l)+cost(l,node_letters[s][j]) <= best[j])
is_best=true;
if (is_best)
node_letters[t].push_back(l);
}
}
return node_letters;
}
B n_mutations(const alignment& A, const SequenceTree& T,const ublas::matrix<B>& cost)
{
const alphabet& a = A.get_alphabet();
vector<int> letters(T.n_leaves());
int root = T.directed_branch(0).target();
vector<const_branchview> branches = branches_toward_node(T,root);
ublas::matrix<B> n_muts(T.n_nodes(), a.size());
double tree_length = 0;
for(int c=0;c<A.length();c++) {
for(int i=0;i<T.n_leaves();i++)
letters[i] = A(c,i);
double length = n_mutations<B>(a,letters,T,cost,n_muts,branches);
tree_length += length;
}
return tree_length;
}
vector<int> get_parsimony_letters(const alphabet& a, const vector<int>& letters, const SequenceTree& T,
const ublas::matrix<int>& cost)
{
int root = T.directed_branch(0).target();
ublas::matrix<int> n_muts(T.n_nodes(),a.size());
peel_n_mutations(a,letters,T,cost,n_muts, branches_toward_node(T,root) );
// get an order list of branches point away from the root;
vector<const_branchview> branches = branches_from_node(T,root);
std::reverse(branches.begin(),branches.end());
// Allocate space to store the letter for each node
vector<int> node_letters(T.n_nodes(),-1);
// choose the cheapest letter at the root
node_letters[root] = row_min(n_muts,root);
const unsigned A = a.size();
vector<double> temp(A);
for(int i=0;i<branches.size();i++)
{
int s = branches[i].source();
int t = branches[i].target();
int k = node_letters[s];
assert(k != -1);
for(int l=0;l<A;l++)
temp[l] = n_muts(t,l)+cost(l,k);
node_letters[t] = argmin(temp);
}
return node_letters;
}
// mark nodes in T according to what node of Q they map to
vector<int> get_nodes_map(const SequenceTree& Q,const SequenceTree& T,
const vector<int>& branches_map)
{
assert(branches_map.size() == Q.n_branches() * 2);
vector<int> nodes_map(T.n_nodes(),-1);
// map nodes from T -> Q that are in both trees
for(int b=0;b<Q.n_branches();b++)
{
int Q_source = Q.branch(b).source();
int Q_target = Q.branch(b).target();
int b2 = branches_map[b];
int T_source = T.directed_branch(b2).source();
int T_target = T.directed_branch(b2).target();
if (nodes_map[T_source] == -1)
nodes_map[T_source] = Q_source;
else
assert(nodes_map[T_source] == Q_source);
if (nodes_map[T_target] == -1)
nodes_map[T_target] = Q_target;
else
assert(nodes_map[T_target] == Q_target);
}
// map the rest of the nodes from T -> Q
for(int i=Q.n_leaves();i<Q.n_nodes();i++)
{
unsigned D = Q[i].degree();
if (D <= 3) continue;
// get a branch of Q pointing into the node
const_branchview outside = *(Q[i].branches_in());
// get a branch of T pointing into the node
outside = T.directed_branch(branches_map[outside.name()]);
list<const_branchview> branches;
typedef list<const_branchview>::iterator list_iterator;
append(outside.branches_after(),branches);
for(list_iterator b = branches.begin() ; b != branches.end();)
{
int node = (*b).target();
if (nodes_map[node] == -1)
nodes_map[node] = i;
if (nodes_map[node] == i) {
append((*b).branches_after(),branches);
b++;
}
else {
list_iterator prev = b;
b++;
branches.erase(prev);
}
}
assert(branches.size() == D-3);
}
for(int i=0;i<nodes_map.size();i++)
assert(nodes_map[i] != -1);
return nodes_map;
}
int main(int argc,char* argv[])
{
try {
//---------- Parse command line -------//
variables_map args = parse_cmd_line(argc,argv);
//----------- Load alignment and tree ---------//
alignment A;
SequenceTree T;
if (args.count("tree"))
load_A_and_T(args,A,T,false);
else
A = load_A(args,false);
const alphabet& a = A.get_alphabet();
//------- Load groups and find branches -------//
vector<sequence_group> groups;
if (args.count("groups"))
groups = load_groups(A,args["groups"].as<string>());
for(int i=0;i<groups.size();i++) {
cerr<<groups[i].name<<": ";
for(int j=0;j<groups[i].taxa.size();j++)
cerr<<A.seq(groups[i].taxa[j]).name<<" ";
cerr<<endl;
}
vector<int> group_branches;
if (args.count("tree"))
{
for(int i=0;i<groups.size();i++)
{
dynamic_bitset<> p(T.n_leaves());
for(int j=0;j<groups[i].taxa.size();j++)
p[groups[i].taxa[j]] = true;
int found = -1;
for(int b=0;b<2*T.n_branches() and found == -1;b++)
if (p == branch_partition(T,b))
found = b;
if (found == -1)
throw myexception()<<"I can't find group "<<i+1<<" on the tree!";
group_branches.push_back(found);
}
}
vector<string> group_names;
for(int i=0;i<groups.size();i++)
group_names.push_back(groups[i].name);
vector<Partition> splits;
if (args.count("split"))
{
vector<string> split = args["split"].as<vector<string> >();
for(int i=0;i<split.size();i++)
splits.push_back(Partition(group_names,split[i]));
}
//-------------------------------------------//
Matrix C(A.length(),A.n_sequences()+1);
for(int i=0;i<C.size1();i++)
for(int j=0;j<C.size2();j++)
C(i,j) = 0;
// yes but, how much more conservation THAN EXPECTED do we see?
for(int c=0;c<C.size1();c++)
{
vector<bool> interesting(groups.size(), true);
//-------------------------------------------------------//
vector<int> leaf_letters( T.n_leaves() );
for(int j=0;j<leaf_letters.size();j++)
leaf_letters[j] = A(c,j);
vector<vector<int> > node_letters = get_all_parsimony_letters(a,leaf_letters,T,unit_cost_matrix(a));
vector<vector<int> > initial_value(groups.size());
for(int g=0;g<groups.size();g++)
{
int n = T.directed_branch(group_branches[g]).target();
initial_value[g] = node_letters[n];
}
//------------ find 'group conserved at' values ----------//
vector<int> value(groups.size(),alphabet::gap);
for(int g=0;g<groups.size();g++)
{
vector<int> temp;
for(int i=0;i<groups[g].taxa.size();i++)
temp.push_back(A(c,groups[g].taxa[i]));
int best = most_common(temp);
int count = number_of(temp,best);
if (count >= groups[g].taxa.size()-1 and count >=3 and count> groups[g].taxa.size()/2)
value[g] = best;
}
//-------- Determine whether column is interesting --------//
if (args.count("require-all-different"))
{
if (args.count("split"))
{
vector<bool> in_changed_split(groups.size(),false);
for(int i=0;i<splits.size();i++)
{
bool some_different = false;
for(int g1=0;g1<groups.size();g1++)
for(int g2=0;g2<groups.size();g2++)
if (splits[i].group1[g1] and splits[i].group2[g2]) {
if (all_different(A,c,groups,g1,g2))
some_different = true;
}
bool no_same = true;
for(int g1=0;g1<groups.size();g1++)
for(int g2=0;g2<groups.size();g2++)
if (splits[i].group1[g1] and splits[i].group2[g2])
if (not all_different(A,c,groups,g1,g2))
no_same = false;
if (some_different and no_same)
for(int g=0;g<groups.size();g++)
if (splits[i].group1[g] or splits[i].group2[g])
in_changed_split[g] = true;
}
for(int g=0;g<groups.size();g++)
interesting[g] = interesting[g] and in_changed_split[g];
}
else {
bool different = false;
for(int g1=0;g1<groups.size();g1++)
for(int g2=0;g2<groups.size();g2++)
if (all_different(A,c,groups,g1,g2))
different = true;
if (not different)
for(int g=0;g<groups.size();g++)
interesting[g] = false;
}
}
if (args.count("require-change"))
{
if (args.count("split"))
{
vector<bool> in_changed_split(groups.size(),false);
for(int i=0;i<splits.size();i++)
{
bool some_different = false;
for(int g1=0;g1<groups.size();g1++)
for(int g2=0;g2<groups.size();g2++)
if (splits[i].group1[g1] and splits[i].group2[g2]) {
if (value[g1] != value[g2])
if (not args.count("ignore-rate-change") or
(value[g1] != alphabet::gap and value[g2] != alphabet::gap))
some_different = true;
}
bool no_same = true;
for(int g1=0;g1<groups.size();g1++)
for(int g2=0;g2<groups.size();g2++)
if (splits[i].group1[g1] and splits[i].group2[g2])
if (value[g1] == value[g2])
no_same = false;
// This is Option #1
// - some conserved differences but no conserved similarities
// Also consider Option #2
// - a change in both LETTER and CONSERVATION on at least one of the
// two branches leading from the duplication.
if (some_different and no_same)
for(int g=0;g<groups.size();g++)
if (splits[i].group1[g] or splits[i].group2[g])
in_changed_split[g] = true;
}
for(int g=0;g<groups.size();g++)
interesting[g] = interesting[g] and in_changed_split[g];
}
else {
if (args.count("ignore-rate-change"))
{
for(int g=0;g<groups.size();g++)
interesting[g] = interesting[g] and not all_same_or(value,alphabet::gap);
}
else
{
for(int g=0;g<groups.size();g++)
interesting[g] = interesting[g] and not all_same(value);
}
}
}
// A group is only interesting if its conserved
if (args.count("require-conservation"))
for(int g=0;g<groups.size();g++)
interesting[g] = interesting[g] and (value[g] != alphabet::gap);
// A group is only interesting if it is in one of the splits
if (args.count("split"))
for(int g=0;g<groups.size();g++) {
bool found = false;
for(int i=0;i<splits.size() and not found;i++)
if (splits[i].group1[g] or splits[i].group2[g])
found = true;
interesting[g] = interesting[g] and found;
}
//------------ print 'group conserved at' values ----------//
cerr<<c+1<<" ";
for(int i=0;i<value.size();i++)
cerr<<a.lookup(value[i])<<" ";
cerr<<" ";
for(int g=0;g<groups.size();g++)
if (interesting[g])
cerr<<"1 ";
else
cerr<<"0 ";
cerr<<endl;
//------------- print parsimony initial values --------------//
cerr<<" ";
for(int i=0;i<initial_value.size();i++) {
for(int j=0;j<initial_value[i].size();j++)
cerr<<a.lookup(initial_value[i][j]);
cerr<<" ";
}
cerr<<" "<<n_mutations(a,leaf_letters,T,unit_cost_matrix(a))<<endl;
cerr<<endl;
//--------------------- Set highlighting ---------------------//
// Interesting groups -> 1.0
for(int g=0;g<groups.size();g++)
if (interesting[g])
for(int i=0;i<groups[g].taxa.size();i++)
C(c,groups[g].taxa[i]) = 1.0;
// Set conserved groups -> 0.5
for(int g=0;g<groups.size();g++)
if (value[g] != alphabet::gap)
for(int i=0;i<groups[g].taxa.size();i++)
C(c,groups[g].taxa[i]) = std::max(0.5, C(c,groups[g].taxa[i]));
}
cout<<join(sequence_names(A),' ')<<endl;
for(int i=0;i<C.size1();i++) {
vector<double> temp;
for(int j=0;j<C.size2();j++)
temp.push_back(C(i,j));
cout<<join(temp,' ')<<endl;
}
}
catch (std::exception& e) {
std::cerr<<"alignment-find-conserved: Error! "<<e.what()<<endl;
exit(1);
}
return 0;
}
