m->openInputFile(fastaFile, in);
map<string, string> seqName; //stores name -> sequence string so we can make new "unique" sequences when we parse the name file
+ int fastaCount = 0;
while (!in.eof()) {
if (m->control_pressed) { break; }
Sequence seq(in); m->gobble(in);
+ fastaCount++;
+ if (m->debug) { if((fastaCount) % 1000 == 0){ m->mothurOut("[DEBUG]: reading seq " + toString(fastaCount) + "\n."); } }
- if (seq.getName() != "") {
+ if (seq.getName() != "") {
string group = groupMap->getGroup(seq.getName());
if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
in.close();
if (error == 1) { m->control_pressed = true; }
-
+
//read name file
ifstream inName;
m->openInputFile(nameFile, inName);
- string first, second;
+ //string first, second;
int countName = 0;
set<string> thisnames1;
- while(!inName.eof()) {
-
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!inName.eof()) {
if (m->control_pressed) { break; }
- inName >> first; m->gobble(inName);
- inName >> second; m->gobble(inName);
-
- vector<string> names;
- m->splitAtChar(second, names, ',');
-
- //get aligned string for these seqs from the fasta file
- string alignedString = "";
- map<string, string>::iterator itAligned = seqName.find(names[0]);
- if (itAligned == seqName.end()) {
- error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
- }else {
- alignedString = itAligned->second;
- }
-
- //separate by group - parse one line in name file
- map<string, string> splitMap; //group -> name1,name2,...
- map<string, string>::iterator it;
- for (int i = 0; i < names.size(); i++) {
-
- string group = groupMap->getGroup(names[i]);
- if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
- else {
-
- it = splitMap.find(group);
- if (it != splitMap.end()) { //adding seqs to this group
- (it->second) += "," + names[i];
- thisnames1.insert(names[i]);
- countName++;
- }else { //first sighting of this group
- splitMap[group] = names[i];
- countName++;
- thisnames1.insert(names[i]);
-
- //is this seq in the fasta file?
- if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
- Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
- seqs[group].push_back(tempSeq);
- }
- }
- }
-
- allSeqsMap[names[i]] = names[0];
- }
-
-
- //fill nameMapPerGroup - holds all lines in namefile separated by group
- for (it = splitMap.begin(); it != splitMap.end(); it++) {
- //grab first name
- string firstName = "";
- for(int i = 0; i < (it->second).length(); i++) {
- if (((it->second)[i]) != ',') {
- firstName += ((it->second)[i]);
- }else { break; }
- }
-
- //group1 -> seq1 -> seq1,seq2,seq3
- nameMapPerGroup[it->first][firstName] = it->second;
- }
+ inName.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, inName.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) { //save one line
+ if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
+ vector<string> names;
+ m->splitAtChar(secondCol, names, ',');
+
+ //get aligned string for these seqs from the fasta file
+ string alignedString = "";
+ map<string, string>::iterator itAligned = seqName.find(names[0]);
+ if (itAligned == seqName.end()) {
+ error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
+ }else {
+ alignedString = itAligned->second;
+ }
+
+ //separate by group - parse one line in name file
+ map<string, string> splitMap; //group -> name1,name2,...
+ map<string, string>::iterator it;
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap->getGroup(names[i]);
+ if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
+ else {
+
+ it = splitMap.find(group);
+ if (it != splitMap.end()) { //adding seqs to this group
+ (it->second) += "," + names[i];
+ thisnames1.insert(names[i]);
+ countName++;
+ }else { //first sighting of this group
+ splitMap[group] = names[i];
+ countName++;
+ thisnames1.insert(names[i]);
+
+ //is this seq in the fasta file?
+ if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
+ Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
+ seqs[group].push_back(tempSeq);
+ }
+ }
+ }
+
+ allSeqsMap[names[i]] = names[0];
+ }
+
+
+ //fill nameMapPerGroup - holds all lines in namefile separated by group
+ for (it = splitMap.begin(); it != splitMap.end(); it++) {
+ //grab first name
+ string firstName = "";
+ for(int i = 0; i < (it->second).length(); i++) {
+ if (((it->second)[i]) != ',') {
+ firstName += ((it->second)[i]);
+ }else { break; }
+ }
+
+ //group1 -> seq1 -> seq1,seq2,seq3
+ nameMapPerGroup[it->first][firstName] = it->second;
+ }
+
+ pairDone = false;
+ }
+ }
}
-
inName.close();
+
+ //in case file does not end in white space
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) { //save one line
+ if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
+ vector<string> names;
+ m->splitAtChar(secondCol, names, ',');
+
+ //get aligned string for these seqs from the fasta file
+ string alignedString = "";
+ map<string, string>::iterator itAligned = seqName.find(names[0]);
+ if (itAligned == seqName.end()) {
+ error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
+ }else {
+ alignedString = itAligned->second;
+ }
+
+ //separate by group - parse one line in name file
+ map<string, string> splitMap; //group -> name1,name2,...
+ map<string, string>::iterator it;
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap->getGroup(names[i]);
+ if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
+ else {
+
+ it = splitMap.find(group);
+ if (it != splitMap.end()) { //adding seqs to this group
+ (it->second) += "," + names[i];
+ thisnames1.insert(names[i]);
+ countName++;
+ }else { //first sighting of this group
+ splitMap[group] = names[i];
+ countName++;
+ thisnames1.insert(names[i]);
+
+ //is this seq in the fasta file?
+ if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
+ Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
+ seqs[group].push_back(tempSeq);
+ }
+ }
+ }
+
+ allSeqsMap[names[i]] = names[0];
+ }
+
+
+ //fill nameMapPerGroup - holds all lines in namefile separated by group
+ for (it = splitMap.begin(); it != splitMap.end(); it++) {
+ //grab first name
+ string firstName = "";
+ for(int i = 0; i < (it->second).length(); i++) {
+ if (((it->second)[i]) != ',') {
+ firstName += ((it->second)[i]);
+ }else { break; }
+ }
+
+ //group1 -> seq1 -> seq1,seq2,seq3
+ nameMapPerGroup[it->first][firstName] = it->second;
+ }
+
+ pairDone = false;
+ }
+ }
+ }
if (error == 1) { m->control_pressed = true; }
-
+
if (countName != (groupMap->getNumSeqs())) {
vector<string> groupseqsnames = groupMap->getNamesSeqs();
+
for (int i = 0; i < groupseqsnames.size(); i++) {
set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
if (itnamesfile == thisnames1.end()){
cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
}
}
+
m->mothurOutEndLine();
m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
m->mothurOutEndLine();
/************************************************************/
bool SequenceParser::isValidGroup(string g){ return groupMap->isValidGroup(g); }
/************************************************************/
-string SequenceParser::getGroup(string g){ return groupMap->getGroup(g); }
-/************************************************************/
int SequenceParser::getNumSeqs(string g){
try {
map<string, vector<Sequence> >::iterator it;
m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
}else {
seqForThisGroup = it->second;
+ if (m->debug) { m->mothurOut("[DEBUG]: group " + g + " fasta file has " + toString(seqForThisGroup.size()) + " sequences."); }
}
return seqForThisGroup;
if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
- out << ">" << nameVector[i].name << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl;
+ out << ">" << nameVector[i].name << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl; //
}
}else {
+ //m->mothurOut("Group " + g + " contains " + toString(seqForThisGroup.size()) + " unique seqs.\n");
for (int i = 0; i < seqForThisGroup.size(); i++) {
if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
}else {
nameMapForThisGroup = it->second;
+ if (m->debug) { m->mothurOut("[DEBUG]: group " + g + " name file has " + toString(nameMapForThisGroup.size()) + " unique sequences."); }
}
return nameMapForThisGroup;
projects / mothur.git / blobdiff