+++ /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);
- }
-}
-
-/**************************************************************************************************/
-
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