static void doAlignments(struct sqlConnection *conn, char *db)
{
int taxon = findTaxon(conn,db);
populateMissingVgPrbAli(conn, taxon, db, "vgPrbAli");
updateVgPrbAli(conn, db, "vgPrbAli","vgProbes");
doAccessionsAli(conn, taxon, db);
doFakeBacAli(conn, taxon, db);
assembleAllPsl(conn, taxon, db);
rollupPsl("vgPrbNonBlat.psl", "vgProbes", conn, db);
updateVgPrbAli(conn, db, "vgPrbAli","vgProbes");
doBlat(conn, taxon, db);
rollupPsl("blatNearBest.psl", "vgProbes", conn, db);
updateVgPrbAli(conn, db, "vgPrbAli","vgProbes");
markNoneVgPrbAli(conn, taxon, db, "vgPrbAli");
}
static void doAlignmentsPslMap(struct sqlConnection *conn, char *db, char *fromDb)
{
int taxon = findTaxon(conn,db);
int fromTaxon = findTaxon(conn,fromDb);
populateMissingVgPrbAli(conn, fromTaxon, db, "vgPrbAliAll");
updateVgPrbAli(conn, db, "vgPrbAliAll","vgAllProbes");
doPslMapAli(conn, taxon, db, fromTaxon, fromDb);
rollupPsl("vgPrbPslMap.psl", "vgAllProbes", conn, db);
updateVgPrbAli(conn, db, "vgPrbAliAll","vgAllProbes");
markNoneVgPrbAli(conn, fromTaxon, db, "vgPrbAliAll");
}
static void doAlignmentsReMap(
struct sqlConnection *conn,
char *db, char *fromDb, char *track, char *fasta)
/* re-map anything in track specified that is not aligned,
nor even attempted yet, using specified fasta file. */
{
int taxon = findTaxon(conn,db);
int fromTaxon = findTaxon(conn,fromDb);
populateMissingVgPrbAli(conn, fromTaxon, db, "vgPrbAliAll");
updateVgPrbAli(conn, db, "vgPrbAliAll","vgAllProbes");
doReMapAli(conn, taxon, db, fromTaxon, fromDb, track, fasta);
rollupPsl("vgPrbReMap.psl", "vgAllProbes", conn, db);
updateVgPrbAli(conn, db, "vgPrbAliAll","vgAllProbes");
markNoneVgPrbAli(conn, fromTaxon, db, "vgPrbAliAll");
}
static void makeFakeProbeSeq(struct sqlConnection *conn, char *db)
/* get probe seq from primers, bacEndPairs, refSeq, genbank, gene-name */
{
int taxon = findTaxon(conn,db);
//restore:
doPrimers(conn, taxon, db);
//restore:
doBacEndPairs(conn, taxon, db);
//restore:
doAccessionsSeq(conn, taxon, db);
}
static void doAlignmentsSelfMap(
struct sqlConnection *conn, char *db)
/* copy anything in vgProbes but not in vgAllProbes to vgAllProbes */
{
int taxon = findTaxon(conn,db);
populateMissingVgPrbAli(conn, taxon, db, "vgPrbAliAll");
updateVgPrbAli(conn, db, "vgPrbAliAll","vgAllProbes");
doSelfMapAli(conn, taxon, db);
rollupPsl("vgPrbSelfMap.psl", "vgAllProbes", conn, db);
updateVgPrbAli(conn, db, "vgPrbAliAll","vgAllProbes");
markNoneVgPrbAli(conn, taxon, db, "vgPrbAliAll");
}
void PhyloSummary::print(int i, ofstream& out, string output){
try {
map<string,int>::iterator it;
for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
if (tree[it->second].total != 0) {
int totalChildrenInTree = 0;
map<string,int>::iterator it2;
for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
if (tree[it2->second].total != 0) { totalChildrenInTree++; }
}
if ((output == "detail") && (printlevel >= tree[it->second].level)) {
if (relabund) {
out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << (tree[it->second].total/(double) tree[0].total);
}else {
out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total;
}
}else {
if (printlevel == tree[it->second].level) { //leaf node - we want to print it. Use rank to find full taxonomy
if (relabund) {
out << findTaxon(tree[it->second].rank) << '\t' << tree[it->second].total/(double) tree[0].total;
}else {
out << findTaxon(tree[it->second].rank) << '\t' << tree[it->second].total;
}
}
}
if (relabund) {
map<string, int>::iterator itGroup;
if (groupmap != NULL) {
vector<string> mGroups = groupmap->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
if (((output == "detail") && (printlevel >= tree[it->second].level)) || (printlevel == tree[it->second].level)) {
out << '\t' << (tree[it->second].groupCount[mGroups[i]]/(double)groupmap->getNumSeqs(mGroups[i]));
}
}
}else if (ct != NULL) {
if (ct->hasGroupInfo()) {
vector<string> mGroups = ct->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
if (((output == "detail") && (printlevel >= tree[it->second].level)) || (printlevel == tree[it->second].level)) {
out << '\t' << (tree[it->second].groupCount[mGroups[i]]/(double)ct->getGroupCount(mGroups[i]));
}
}
}
}
}else {
map<string, int>::iterator itGroup;
if (groupmap != NULL) {
vector<string> mGroups = groupmap->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
if (((output == "detail") && (printlevel >= tree[it->second].level)) || (printlevel == tree[it->second].level)) {
out << '\t' << tree[it->second].groupCount[mGroups[i]];
}
}
}else if (ct != NULL) {
if (ct->hasGroupInfo()) {
vector<string> mGroups = ct->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
if (((output == "detail") && (printlevel >= tree[it->second].level)) || (printlevel == tree[it->second].level)) {
out << '\t' << tree[it->second].groupCount[mGroups[i]];
}
}
}
}
}
if (((output == "detail") && (printlevel >= tree[it->second].level)) || (printlevel == tree[it->second].level)) { out << endl; }
}
print(it->second, out, output);
}
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "print");
exit(1);
}
}
