@@ -53,6 +53,8 @@ using namespace std;
#include " SQLiteProfiler.h"
#define SIXES 666666
template <class T >
inline std::string to_string (const T& t)
{
@@ -68,9 +70,11 @@ SQLiteProfiler::SQLiteProfiler(string gn, string cn, string dbs,bool autom,bool
db = dbs;
automated = autom;
updatedb = updb;
usertree = false ;
profilefoldername = gene_name+" _PROFILE/"
}
// TODO: add the ability to have the usertree inform these alignments
void SQLiteProfiler::prelimalign (){
// if temp directory doesn't exist
mkdir (profilefoldername.c_str (),S_IRWXU | S_IRWXG | S_IROTH | S_IWOTH);
@@ -292,6 +296,9 @@ void SQLiteProfiler::prelimalign(){
}
}
/*
* TODO: probably better to have a operating system independent one
*/
int SQLiteProfiler::count_seqs (string dirc, string file_name){
string cmd = " grep -c \\ > "
cmd += dirc+" /"
@@ -310,31 +317,24 @@ int SQLiteProfiler::count_seqs(string dirc, string file_name){
return intReturn;
}
void SQLiteProfiler::set_user_guide_tree (Tree * tree){
usertree = true ;
userguidetree = tree;
}
void SQLiteProfiler::run (){
if (updatedb == false ){// standard
file_names = vector<string>();
cout << " getting file names"
getdir (profilefoldername.c_str (),file_names);
if (file_names.size () > 1 ){
// get guide tree
// if the guide tree is not there, then use the ncbi tree
string guiname = gene_name+" .guide"
bool flag = false ;
fstream fin;
fin.open (guiname.c_str (),ios::in);
if ( fin.is_open () ){
flag=true ;
}
fin.close ();
// end test for guide tree
map<string,string> numnames;
map<string,string> namesnum;
vector< vector<double > > numlist;
// TODO: add incomplete user guide tree
if (flag == true ){
// TODO: make sure that this works with update , incomplete user guide tree
if (usertree == true ){
cout << " user guide tree"
Tree * tree = read_user_guide_tree (guiname);
create_distances (file_names,tree,&numnames,&namesnum,&numlist);
create_distances_user_tree (file_names,&numnames,&namesnum,&numlist);
}else {// use ncbi tree
cout << " ncbi guide tree"
create_distances (cladename,file_names,&numnames,&namesnum,&numlist);
@@ -381,39 +381,6 @@ string SQLiteProfiler::get_profilekey_value(string profile_string){
return match_string;
}
Tree * SQLiteProfiler::read_user_guide_tree (string filen){
TreeReader nw;
ifstream infile2 (filen.c_str ());
vector<string> lines;
string line;
while (getline (infile2, line)){
lines.push_back (line);
}
infile2.close ();
Tree * tree = nw.readTree (lines[0 ]);
vector<string> orphans;
for (int i=0 ;i<file_names.size ();i++){
try {
tree->getExternalNode (file_names[i])->getName ();
}catch (int e){
orphans.push_back (file_names[i]);
use_orphan = true ;
}
}
string orphfilename = profilefoldername+" orphan"
ofstream myfile (orphfilename.c_str ());
for (int i=0 ;i<orphans.size ();i++){
ifstream tfile (orphans[i].c_str ());
string line;
while (getline (tfile,line)){
myfile << line; // make sure it adds the \n
}
}
myfile.close ();
return tree;
}
void SQLiteProfiler::get_children (string in_id, vector<string> * in_ids, vector<string> * in_keepids){
Database conn (db);
string sql = " SELECT ncbi_id FROM taxonomy WHERE parent_ncbi_id = "
@@ -564,74 +531,40 @@ void SQLiteProfiler::create_distances(string clade_name, vector<string> names,ma
for (int i=0 ;i<names.size ();i++){
Database conn (db);
sql = " SELECT ncbi_id FROM taxonomy WHERE name = '" " ' and name_class = 'scientific name';"
// cout << sql << endl;
Query query2 (conn);
query2.get_result (sql);
// StoreQueryResult R = query2.store();
string nameid = get_right_one (allids, query2);
sql = " SELECT parent_ncbi_id FROM taxonomy WHERE ncbi_id = " " and name_class = 'scientific name';"
Query query4 (conn);
query4.get_result (sql);
// StoreQueryResult R2 = query4.store();
string parentid = get_right_one (allids,query4);
vector<string> route;
while (parentid != cladeid){
// cout << "loop" << endl;
route.push_back (parentid);
cout << " nameid "
cout << " parentid1 "
// cout << "nameid " << nameid << endl;
// cout << "parentid1 " << parentid << endl;
nameid = parentid;
sql = " SELECT parent_ncbi_id FROM taxonomy WHERE ncbi_id = " " and name_class = 'scientific name';"
// cout << sql << endl;
Query query5 (conn);
query5.get_result (sql);
// StoreQueryResult R3 = query5.store();
parentid = get_right_one (allids,query5);
// cout << "parentid2 " << parentid << endl;
}
route.push_back (parentid);
/*
* add using the left right for the route
*
string left,right;
sql = "SELECT left_value,right_value FROM taxon WHERE taxon.taxon_id = "+nameid;
Query query5 = conn.query(sql);
StoreQueryResult R3 = query5.store();
left = R3[0][0].c_str();
right = R3[0][1].c_str();
vector<string> route;
sql = "SELECT taxon.taxon_id FROM taxon WHERE left_value < "+left;
sql += "AND right_value > ";
sql += right;
sql+= "AND left_value >= ";
sql+= cladeleft;
sql+= "AND right_value <= ";
sql += claderight;
sql += "ORDER BY left_value DESC;";
Query query4 = conn.query(sql);
StoreQueryResult R2 = query4.store();
for(int j=0;j<R2.size();j++){
route.push_back(R2[j][0].c_str());
}
*
* end add
*/
vector<double > tdistance;
for (int j=0 ;j<names.size ();j++){
if (j!=i){
sql = " SELECT ncbi_id FROM taxonomy WHERE name = '" " ' and name_class = 'scientific name';"
Query query5 (conn);
query5.get_result (sql);
// StoreQueryResult R3 = query5.store();
string jnameid = get_right_one (allids,query5);
double distance = 0 ;
while ((int )count (route.begin (),route.end (),jnameid) == 0 ){
distance += 1 ;
sql = " SELECT parent_ncbi_id FROM taxonomy WHERE ncbi_id = " " and name_class = 'scientific name';"
Query query6 (conn);
query6.get_result (sql);
// StoreQueryResult R4 = query6.store();
jnameid = get_right_one (allids,query6);
}
for (int k=0 ;k<route.size ();k++){
@@ -640,7 +573,7 @@ void SQLiteProfiler::create_distances(string clade_name, vector<string> names,ma
}
tdistance.push_back (distance);
}else {
tdistance.push_back (666666 );
tdistance.push_back (SIXES );
}
}
std::ostringstream stm;
@@ -650,28 +583,33 @@ void SQLiteProfiler::create_distances(string clade_name, vector<string> names,ma
numlist->push_back (tdistance);
cout << " distances complete: "
}
// distances = list(tdistance)
}
// user tree one
void SQLiteProfiler::create_distances (vector<string> names,Tree * tree ,map<string,string> * numnames
void SQLiteProfiler::create_distances_user_tree (vector<string> file_names ,map<string,string> * numnames
,map<string,string> * namesnum, vector< vector<double > > * numlist){
for (int i=0 ;i<names.size ();i++){
Node * nd1 = tree->getExternalNode (names[i]);
// get the list of nodes for which distances are required
vector<Node *> nodesfordist;
for (int i=0 ;i<file_names.size ();i++){
for (int j=0 ;j<userguidetree->getNodeCount ();j++){
if (userguidetree->getNode (j)->getName ()==file_names[i])
nodesfordist.push_back (userguidetree->getNode (j));
}
}
for (int i=0 ;i<nodesfordist.size ();i++){
vector<double > tdistance;
for (int j=0 ;j<names .size ();j++){
for (int j=0 ;j<nodesfordist .size ();j++){
if (i == j){
tdistance.push_back (666666 );
tdistance.push_back (SIXES );
}else {
Node * nd2 = tree->getExternalNode (names[j]);
double distance = get_distance_between_two_nodes (tree,nd1,nd2);
double distance = get_distance_between_two_nodes (userguidetree,nodesfordist[i],nodesfordist[j]);
tdistance.push_back (distance);
}
}
std::ostringstream stm;
stm << i;
numnames->insert ( pair<string,string>(stm.str (),names [i]) );
namesnum->insert ( pair<string,string>(names [i],stm.str ()) );
numnames->insert ( pair<string,string>(stm.str (),nodesfordist [i]-> getName () ) );
namesnum->insert ( pair<string,string>(nodesfordist [i]-> getName () ,stm.str ()) );
numlist->push_back (tdistance);
}
}
@@ -691,7 +629,7 @@ void SQLiteProfiler::get_shortest_distance_with_dicts(vector<string> names, map<
for (int j=0 ;j<file_names.size ();j++){
string nameid2 = namesnum[file_names[j]];
double distance = tdistance[atoi (nameid2.c_str ())];
if (distance < shortestdistance && distance != 666666 ){
if (distance < shortestdistance && distance != SIXES ){
shortestdistance = distance;
*shortestnameone = names[i];
keepD = true ;
@@ -704,7 +642,7 @@ void SQLiteProfiler::get_shortest_distance_with_dicts(vector<string> names, map<
shortestnametwo->clear ();
for (int j=0 ;j<file_names.size ();j++){
// int ct = (int) count(shortestnametwo->begin(),shortestnametwo->end(),file_names[j]);
if (distances[j]==shortestdistance && distances[j]!=666666 ){
if (distances[j]==shortestdistance && distances[j]!=SIXES ){
shortestnametwo->push_back (file_names[j]);
cout << " f "
}