--- /dev/null
+/*
+ * ryanscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/23/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "clusterfragmentscommand.h"
+#include "needlemanoverlap.hpp"
+
+//**********************************************************************************************************************
+//sort by unaligned
+inline bool comparePriority(seqRNode first, seqRNode second) {
+ bool better = false;
+
+ if (first.length > second.length) {
+ better = true;
+ }else if (first.length == second.length) {
+ if (first.numIdentical > second.numIdentical) {
+ better = true;
+ }
+ }
+
+ return better;
+}
+//**********************************************************************************************************************
+vector<string> ClusterFragmentsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
+ CommandParameter ppercent("percent", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppercent);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClusterFragmentsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The cluster.fragments command groups sequences that are part of a larger sequence.\n";
+ helpString += "The cluster.fragments command outputs a new fasta and name file.\n";
+ helpString += "The cluster.fragments command parameters are fasta, name, diffs and percent. The fasta parameter is required, unless you have a valid current file. \n";
+ helpString += "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";
+ helpString += "The diffs parameter allows you to set the number of differences allowed, default=0. \n";
+ helpString += "The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster.\n";
+ helpString += "You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge. \n";
+ helpString += "The cluster.fragments command should be in the following format: \n";
+ helpString += "cluster.fragments(fasta=yourFastaFile, names=yourNamesFile) \n";
+ helpString += "Example cluster.fragments(fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClusterFragmentsCommand::ClusterFragmentsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "ClusterFragmentsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
+ if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else if (fastafile == "not open") { fastafile = ""; abort = true; }
+ else { m->setFastaFile(fastafile); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
+
+ //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") { namefile = ""; abort = true; }
+ else { readNameFile(); m->setNameFile(namefile); }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, diffs);
+
+ temp = validParameter.validFile(parameters, "percent", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, percent);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "ClusterFragmentsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ClusterFragmentsCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int start = time(NULL);
+
+ //reads fasta file and return number of seqs
+ int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
+
+ if (m->control_pressed) { return 0; }
+
+ if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; }
+
+ //sort seqs by length of unaligned sequence
+ sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
+
+ int count = 0;
+
+ //think about running through twice...
+ for (int i = 0; i < numSeqs; i++) {
+
+ if (alignSeqs[i].active) { //this sequence has not been merged yet
+
+ string iBases = alignSeqs[i].seq.getUnaligned();
+
+ //try to merge it with all smaller seqs
+ for (int j = i+1; j < numSeqs; j++) {
+
+ if (m->control_pressed) { return 0; }
+
+ if (alignSeqs[j].active) { //this sequence has not been merged yet
+
+ string jBases = alignSeqs[j].seq.getUnaligned();
+
+ if (isFragment(iBases, jBases)) {
+ //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) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+ }
+
+ if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+
+
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+
+ string newFastaFile = fileroot + "fragclust.fasta";
+ string newNamesFile = fileroot + "fragclust.names";
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Total number of sequences before cluster.fragments was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+ m->mothurOut("cluster.fragments removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ printData(newFastaFile, newNamesFile);
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+
+ if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(newFastaFile); m->mothurOutEndLine();
+ m->mothurOut(newNamesFile); m->mothurOutEndLine();
+ outputNames.push_back(newFastaFile); outputNames.push_back(newNamesFile); outputTypes["fasta"].push_back(newFastaFile); outputTypes["name"].push_back(newNamesFile);
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "execute");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+bool ClusterFragmentsCommand::isFragment(string seq1, string seq2){
+ try {
+ bool fragment = false;
+
+ //exact match
+ int pos = seq1.find(seq2);
+ if (pos != string::npos) { return true; }
+ //no match, no diffs wanted
+ else if ((diffs == 0) && (percent == 0)) { return false; }
+ else { //try aligning and see if you can find it
+
+ //find number of acceptable differences for this sequence fragment
+ int totalDiffs;
+ if (diffs == 0) { //you didnt set diffs you want a percentage
+ totalDiffs = floor((seq2.length() * (percent / 100.0)));
+ }else if (percent == 0) { //you didn't set percent you want diffs
+ totalDiffs = diffs;
+ }else if ((percent != 0) && (diffs != 0)) { //you want both, set total diffs to smaller of 2
+ totalDiffs = diffs;
+ int percentDiff = floor((seq2.length() * (percent / 100.0)));
+ if (percentDiff < totalDiffs) { totalDiffs = percentDiff; }
+ }
+
+ Alignment* alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (seq1.length()+totalDiffs+1));
+
+ //use needleman to align
+ alignment->align(seq2, seq1);
+ string tempSeq2 = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ delete alignment;
+
+ //chop gap ends
+ int startPos = 0;
+ int endPos = tempSeq2.length()-1;
+ for (int i = 0; i < tempSeq2.length(); i++) { if (isalpha(tempSeq2[i])) { startPos = i; break; } }
+ for (int i = tempSeq2.length()-1; i >= 0; i--) { if (isalpha(tempSeq2[i])) { endPos = i; break; } }
+
+ //count number of diffs
+ int numDiffs = 0;
+ for (int i = startPos; i <= endPos; i++) {
+ if (tempSeq2[i] != temp[i]) { numDiffs++; }
+ }
+
+ if (numDiffs <= totalDiffs) { fragment = true; }
+
+ }
+
+ return fragment;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "isFragment");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int ClusterFragmentsCommand::readFASTA(){
+ try {
+
+ ifstream inFasta;
+ m->openInputFile(fastafile, inFasta);
+
+ while (!inFasta.eof()) {
+
+ if (m->control_pressed) { inFasta.close(); return 0; }
+
+ Sequence seq(inFasta); m->gobble(inFasta);
+
+ 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{
+ seqRNode tempNode(itSize->second, seq, names[seq.getName()], seq.getUnaligned().length());
+ alignSeqs.push_back(tempNode);
+ }
+ }else { //no names file, you are identical to yourself
+ seqRNode tempNode(1, seq, seq.getName(), seq.getUnaligned().length());
+ alignSeqs.push_back(tempNode);
+ }
+ }
+ }
+
+ inFasta.close();
+ return alignSeqs.size();
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "readFASTA");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void ClusterFragmentsCommand::printData(string newfasta, string newname){
+ try {
+ ofstream outFasta;
+ ofstream outNames;
+
+ m->openOutputFile(newfasta, outFasta);
+ m->openOutputFile(newname, outNames);
+
+ 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;
+ }
+ }
+
+ outFasta.close();
+ outNames.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "printData");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void ClusterFragmentsCommand::readNameFile(){
+ try {
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ in >> firstCol >> secondCol; m->gobble(in);
+ names[firstCol] = secondCol;
+ int size = 1;
+
+ for(int i=0;i<secondCol.size();i++){
+ if(secondCol[i] == ','){ size++; }
+ }
+ sizes[firstCol] = size;
+ }
+ in.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "readNameFile");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+