//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
namefile = validParameter.validFile(parameters, "name", true);
+
if (namefile == "not found") { namefile = ""; }
else if (namefile == "not open") { abort = true; }
- else { readNameFile(); }
+// else { readNameFile(); }
string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
convert(temp, diffs);
if (abort == true) { return 0; }
//reads fasta file and return number of seqs
- int numSeqs = readSeqs(); //fills alignSeqs and makes all seqs active
+ int numSeqs = readNamesFASTA(); //fills alignSeqs and makes all seqs active
if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0; }
if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); return 0; }
//clear sizes since you only needed this info to build the alignSeqs seqPNode structs
- sizes.clear();
+// sizes.clear();
//sort seqs by number of identical seqs
sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
//go through active list and cluster everthing you can, until all nodes are inactive
//taking advantage of the fact that maps are already sorted
- map<string, bool>::iterator itActive;
- map<string, bool>::iterator it2Active;
+// map<string, bool>::iterator itActive;
+// map<string, bool>::iterator it2Active;
int count = 0;
- for (int i = 0; i < alignSeqs.size(); i++) {
-
- //are you active
- itActive = active.find(alignSeqs[i].seq.getName());
+ for (int i = 0; i < numSeqs; i++) {
- if (itActive != active.end()) { //this sequence has not been merged yet
+ //are you active
+ // itActive = active.find(alignSeqs[i].seq.getName());
- //try to merge it with all smaller seqs
- for (int j = i; j < alignSeqs.size(); j++) {
-
- if (i != j) {
- //are you active
- it2Active = active.find(alignSeqs[j].seq.getName());
- if (it2Active != active.end()) { //this sequence has not been merged yet
- //are you within "diff" bases
- int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
-
- if (mismatch <= diffs) {
- //merge
- names[alignSeqs[i].seq.getName()] += "," + names[alignSeqs[j].seq.getName()];
-
- //remove from active list
- active.erase(it2Active);
-
- //set numIdentical to 0, so you only print the representative seqs in the fasta file
- alignSeqs[j].numIdentical = 0;
- count++;
- }
- }//end if j active
- }//end if i != j
- }//end for loop
+ if (alignSeqs[i].active) { //this sequence has not been merged yet
- //remove from active list
- active.erase(itActive);
+ //try to merge it with all smaller seqs
+ for (int j = i+1; j < numSeqs; j++) {
+ if (alignSeqs[j].active) { //this sequence has not been merged yet
+ //are you within "diff" bases
+ int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
+
+ if (mismatch <= diffs) {
+ //merge
+ alignSeqs[i].names += ',' + alignSeqs[j].names;
+ alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
+
+ alignSeqs[j].active = 0;
+ alignSeqs[j].numIdentical = 0;
+ count++;
+ }
+ }//end if j active
+ }//end if i != j
+
+ //remove from active list
+ alignSeqs[i].active = 0;
}//end if active i
+ if(i % 100 == 0) { cout << i << '\t' << numSeqs - count << '\t' << count << endl; }
}
string newFastaFile = getRootName(fastafile) + "precluster" + getExtension(fastafile);
string newNamesFile = getRootName(fastafile) + "precluster.names";
- printData(newFastaFile, newNamesFile);
mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();
mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine();
-
+ printData(newFastaFile, newNamesFile);
+
return 0;
}
}
}
/**************************************************************************************************/
-int PreClusterCommand::readSeqs(){
+int PreClusterCommand::readFASTA(){
try {
- ifstream inFasta;
- openInputFile(fastafile, inFasta);
- length = 0;
- map<string, string>::iterator it;
-
- while (!inFasta.eof()) {
- Sequence temp(inFasta); //read seq
-
- if (temp.getName() != "") {
- if (namefile != "") {
- //make sure fasta and name files match
- it = names.find(temp.getName());
- if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
- }else { sizes[temp.getName()] = 1; }
-
- seqPNode tempNode(sizes[temp.getName()], temp);
- alignSeqs.push_back(tempNode);
- active[temp.getName()] = true;
- }
- gobble(inFasta);
- }
- inFasta.close();
-
- if (alignSeqs.size() != 0) { length = alignSeqs[0].seq.getAligned().length(); }
-
+// ifstream inFasta;
+// openInputFile(fastafile, inFasta);
+// length = 0;
+//// map<string, string>::iterator it;
+//
+// while (!inFasta.eof()) {
+// Sequence temp(inFasta); //read seq
+//
+// if (temp.getName() != "") {
+// if (namefile != "") {
+// //make sure fasta and name files match
+// it = names.find(temp.getName());
+// if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
+// }else { sizes[temp.getName()] = 1; }
+//
+// seqPNode tempNode(sizes[temp.getName()], temp);
+// alignSeqs.push_back(tempNode);
+// active[temp.getName()] = true;
+// }
+// gobble(inFasta);
+// }
+// inFasta.close();
+//
+// if (alignSeqs.size() != 0) { length = alignSeqs[0].seq.getAligned().length(); }
+//
return alignSeqs.size();
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readSeqs");
+ errorOut(e, "PreClusterCommand", "readFASTA");
exit(1);
}
}
/**************************************************************************************************/
-void PreClusterCommand::readNameFile(){
+
+int PreClusterCommand::readNamesFASTA(){
try {
- ifstream in;
- openInputFile(namefile, in);
- string firstCol, secondCol;
-
- while (!in.eof()) {
- in >> firstCol >> secondCol; gobble(in);
- names[firstCol] = secondCol;
+ ifstream inNames;
+ ifstream inFasta;
+
+ openInputFile(namefile, inNames);
+ openInputFile(fastafile, inFasta);
+
+ string firstCol, secondCol, nameString;
+ length = 0;
+
+ while (inFasta && inNames) {
+
+ inNames >> firstCol >> secondCol;
+ nameString = secondCol;
+
+ gobble(inNames);
int size = 1;
while (secondCol.find_first_of(',') != -1) {
size++;
secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
}
- sizes[firstCol] = size;
+ Sequence seq(inFasta);
+ if (seq.getName() != firstCol) { mothurOut(seq.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
+ else{
+ seqPNode tempNode(size, seq, nameString);
+ alignSeqs.push_back(tempNode);
+ if (seq.getAligned().length() > length) { length = alignSeqs[0].seq.getAligned().length(); }
+ }
}
- in.close();
+ inFasta.close();
+ inNames.close();
+ return alignSeqs.size();
}
+
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readNameFile");
+ errorOut(e, "PreClusterCommand", "readNamesFASTA");
exit(1);
}
}
+
/**************************************************************************************************/
+
int PreClusterCommand::calcMisMatches(string seq1, string seq2){
try {
int numBad = 0;
exit(1);
}
}
+
/**************************************************************************************************/
+
void PreClusterCommand::printData(string newfasta, string newname){
try {
ofstream outFasta;
ofstream outNames;
+
openOutputFile(newfasta, outFasta);
openOutputFile(newname, outNames);
- map<string, string>::iterator itNames;
for (int i = 0; i < alignSeqs.size(); i++) {
if (alignSeqs[i].numIdentical != 0) {
alignSeqs[i].seq.printSequence(outFasta);
-
- itNames = names.find(alignSeqs[i].seq.getName());
-
- outNames << itNames->first << '\t' << itNames->second << endl;
+ outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
}
}
projects / mothur.git / commitdiff