inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); }
//**********************************************************************************************************************
-PreClusterCommand::PreClusterCommand(string option){
+PreClusterCommand::PreClusterCommand(string option) {
try {
abort = false;
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the pre.cluster command."); m->mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
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);
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "PreClusterCommand");
+ m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
exit(1);
}
}
void PreClusterCommand::help(){
try {
- mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
- mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
- mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
- mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
- mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
- mothurOut("The pre.cluster command should be in the following format: \n");
- mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
- mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ m->mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
+ m->mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
+ m->mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
+ m->mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
+ m->mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
+ m->mothurOut("The pre.cluster command should be in the following format: \n");
+ m->mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
+ m->mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "help");
+ m->errorOut(e, "PreClusterCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
//reads fasta file and return number of seqs
- 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; }
+ int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
- //clear sizes since you only needed this info to build the alignSeqs seqPNode structs
-// sizes.clear();
+ if (m->control_pressed) { return 0; }
+ if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; }
+ if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; }
+
+ string fileroot = outputDir + getRootName(getSimpleName(fastafile));
+ string newFastaFile = fileroot + "precluster" + getExtension(fastafile);
+ string newNamesFile = fileroot + "precluster.names";
+ ofstream outFasta;
+ ofstream outNames;
+
+ openOutputFile(newFastaFile, outFasta);
+ openOutputFile(newNamesFile, outNames);
+
//sort seqs by number of identical seqs
- sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
+ alignSeqs.sort(comparePriority);
int count = 0;
+ int i = 0;
//think about running through twice...
- for (int i = 0; i < numSeqs; i++) {
-
- //are you active
- // itActive = active.find(alignSeqs[i].seq.getName());
-
- if (alignSeqs[i].active) { //this sequence has not been merged yet
-
- //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());
+ list<seqPNode>::iterator itList;
+ list<seqPNode>::iterator itList2;
+ for (itList = alignSeqs.begin(); itList != alignSeqs.end(); itList++) {
+ //try to merge it with all smaller seqs
+ for (itList2 = alignSeqs.begin(); itList2 != alignSeqs.end(); itList2++) {
+
+ if (m->control_pressed) { outFasta.close(); outNames.close(); remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+
+ if ((*itList).seq.getName() != (*itList2).seq.getName()) { //you don't want to merge with yourself
+ //are you within "diff" bases
+ int mismatch = calcMisMatches((*itList).seq.getAligned(), (*itList2).seq.getAligned());
- if (mismatch <= diffs) {
- //merge
- alignSeqs[i].names += ',' + alignSeqs[j].names;
- alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
+ if (mismatch <= diffs) {
+ //merge
+ (*itList).names += ',' + (*itList2).names;
+ (*itList).numIdentical += (*itList2).numIdentical;
- alignSeqs[j].active = 0;
- alignSeqs[j].numIdentical = 0;
- count++;
- }
- }//end if j active
- }//end if i != j
+ alignSeqs.erase(itList2); itList2--;
+ count++;
+ }
+ }
+ }
+
+ //ouptut this sequence
+ printData(outFasta, outNames, (*itList));
+
+ //remove sequence
+ alignSeqs.erase(itList); itList--;
+
+ i++;
- //remove from active list
- alignSeqs[i].active = 0;
- }//end if active i
- if(i % 100 == 0) { cout << i << '\t' << numSeqs - count << '\t' << count << endl; }
+ if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
}
+
+ if(i % 100 != 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
- string fileroot = outputDir + getRootName(getSimpleName(fastafile));
+ outFasta.close();
+ outNames.close();
- string newFastaFile = fileroot + "precluster" + getExtension(fastafile);
- string newNamesFile = fileroot + "precluster.names";
+ if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+
+ m->mothurOut("Total number of sequences before precluster was " + toString(numSeqs) + "."); m->mothurOutEndLine();
+ m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine();
- mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();
- mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine();
- printData(newFastaFile, newNamesFile);
+ if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(newFastaFile); m->mothurOutEndLine();
+ m->mothurOut(newNamesFile); m->mothurOutEndLine();
+ m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "execute");
+ m->errorOut(e, "PreClusterCommand", "execute");
exit(1);
}
}
+
/**************************************************************************************************/
+
+//this requires the names and fasta file to be in the same order
+
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(); }
-//
- return alignSeqs.size();
- }
- catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readFASTA");
- exit(1);
- }
-}
-/**************************************************************************************************/
-//this seems to require the names and fasta file to be in the same order???
-int PreClusterCommand::readNamesFASTA(){
- try {
- ifstream inNames;
+ //ifstream inNames;
ifstream inFasta;
- openInputFile(namefile, inNames);
+ //openInputFile(namefile, inNames);
openInputFile(fastafile, inFasta);
- string firstCol, secondCol, nameString;
+ //string firstCol, secondCol, nameString;
length = 0;
- while (inFasta && inNames) {
-
- inNames >> firstCol >> secondCol;
- nameString = secondCol;
+ while (!inFasta.eof()) {
- gobble(inNames);
- int size = 1;
- while (secondCol.find_first_of(',') != -1) {
- size++;
- secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
- }
+ if (m->control_pressed) { inFasta.close(); return 0; }
+
+ //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());
+ //}
Sequence seq(inFasta); gobble(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(); }
- }
+
+ if (seq.getName() != "") { //can get "" if commented line is at end of fasta file
+ if (namefile != "") {
+ itSize = sizes.find(seq.getName());
+
+ if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
+ else{
+ seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
+ alignSeqs.push_back(tempNode);
+ if (seq.getAligned().length() > length) { length = seq.getAligned().length(); }
+ }
+ }else { //no names file, you are identical to yourself
+ seqPNode tempNode(1, seq, seq.getName());
+ alignSeqs.push_back(tempNode);
+ if (seq.getAligned().length() > length) { length = seq.getAligned().length(); }
+ }
+ }
}
inFasta.close();
- inNames.close();
+ //inNames.close();
return alignSeqs.size();
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readNamesFASTA");
+ m->errorOut(e, "PreClusterCommand", "readFASTA");
exit(1);
}
}
return numBad;
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "calcMisMatches");
+ m->errorOut(e, "PreClusterCommand", "calcMisMatches");
exit(1);
}
}
/**************************************************************************************************/
-void PreClusterCommand::printData(string newfasta, string newname){
+void PreClusterCommand::printData(ofstream& outFasta, ofstream& outNames, seqPNode thisSeq){
try {
- ofstream outFasta;
- ofstream outNames;
-
- openOutputFile(newfasta, outFasta);
- openOutputFile(newname, outNames);
+ thisSeq.seq.printSequence(outFasta);
+ outNames << thisSeq.seq.getName() << '\t' << thisSeq.names << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "printData");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void PreClusterCommand::readNameFile(){
+ try {
+ ifstream in;
+ openInputFile(namefile, in);
+ string firstCol, secondCol;
-
- for (int i = 0; i < alignSeqs.size(); i++) {
- if (alignSeqs[i].numIdentical != 0) {
- alignSeqs[i].seq.printSequence(outFasta);
- outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
+ while (!in.eof()) {
+ in >> firstCol >> secondCol; gobble(in);
+ names[firstCol] = secondCol;
+ int size = 1;
+ while (secondCol.find_first_of(',') != -1) {
+ size++;
+ secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
}
+ sizes[firstCol] = size;
}
-
- outFasta.close();
- outNames.close();
-
+ in.close();
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "printData");
+ m->errorOut(e, "PreClusterCommand", "readNameFile");
exit(1);
}
}
projects / mothur.git / blobdiff