2 * preclustercommand.cpp
5 * Created by westcott on 12/21/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
10 #include "preclustercommand.h"
12 //**********************************************************************************************************************
13 inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); }
14 //**********************************************************************************************************************
16 PreClusterCommand::PreClusterCommand(string option){
20 //allow user to run help
21 if(option == "help") { help(); abort = true; }
24 //valid paramters for this command
25 string Array[] = {"fasta", "name", "diffs"};
26 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
28 OptionParser parser(option);
29 map<string, string> parameters = parser.getParameters();
31 ValidParameters validParameter;
33 //check to make sure all parameters are valid for command
34 for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
35 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
38 //check for required parameters
39 fastafile = validParameter.validFile(parameters, "fasta", true);
40 if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; }
41 else if (fastafile == "not open") { abort = true; }
43 //check for optional parameter and set defaults
44 // ...at some point should added some additional type checking...
45 namefile = validParameter.validFile(parameters, "name", true);
46 if (namefile == "not found") { namefile = ""; }
47 else if (namefile == "not open") { abort = true; }
48 else { readNameFile(); }
50 string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
56 errorOut(e, "PreClusterCommand", "PreClusterCommand");
61 //**********************************************************************************************************************
62 PreClusterCommand::~PreClusterCommand(){}
63 //**********************************************************************************************************************
65 void PreClusterCommand::help(){
67 mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
68 mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
69 mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
70 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");
71 mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
72 mothurOut("The pre.cluster command should be in the following format: \n");
73 mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
74 mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
75 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
78 errorOut(e, "PreClusterCommand", "help");
82 //**********************************************************************************************************************
84 int PreClusterCommand::execute(){
87 if (abort == true) { return 0; }
89 //reads fasta file and return number of seqs
90 int numSeqs = readSeqs(); //fills alignSeqs and makes all seqs active
92 if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0; }
93 if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); return 0; }
95 //clear sizes since you only needed this info to build the alignSeqs seqPNode structs
98 //sort seqs by number of identical seqs
99 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
101 //go through active list and cluster everthing you can, until all nodes are inactive
102 //taking advantage of the fact that maps are already sorted
103 map<string, bool>::iterator itActive;
104 map<string, bool>::iterator it2Active;
107 for (int i = 0; i < alignSeqs.size(); i++) {
110 itActive = active.find(alignSeqs[i].seq.getName());
112 if (itActive != active.end()) { //this sequence has not been merged yet
114 //try to merge it with all smaller seqs
115 for (int j = i; j < alignSeqs.size(); j++) {
119 it2Active = active.find(alignSeqs[j].seq.getName());
120 if (it2Active != active.end()) { //this sequence has not been merged yet
121 //are you within "diff" bases
122 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
124 if (mismatch <= diffs) {
126 names[alignSeqs[i].seq.getName()] += "," + names[alignSeqs[j].seq.getName()];
128 //remove from active list
129 active.erase(it2Active);
131 //set numIdentical to 0, so you only print the representative seqs in the fasta file
132 alignSeqs[j].numIdentical = 0;
139 //remove from active list
140 active.erase(itActive);
144 string newFastaFile = getRootName(fastafile) + "precluster" + getExtension(fastafile);
145 string newNamesFile = getRootName(fastafile) + "precluster.names";
147 printData(newFastaFile, newNamesFile);
149 mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();
150 mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine();
155 catch(exception& e) {
156 errorOut(e, "PreClusterCommand", "execute");
160 /**************************************************************************************************/
161 int PreClusterCommand::readSeqs(){
164 openInputFile(fastafile, inFasta);
166 map<string, string>::iterator it;
168 while (!inFasta.eof()) {
169 Sequence temp(inFasta); //read seq
171 if (temp.getName() != "") {
172 if (namefile != "") {
173 //make sure fasta and name files match
174 it = names.find(temp.getName());
175 if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
176 }else { sizes[temp.getName()] = 1; }
178 seqPNode tempNode(sizes[temp.getName()], temp);
179 alignSeqs.push_back(tempNode);
180 active[temp.getName()] = true;
186 if (alignSeqs.size() != 0) { length = alignSeqs[0].seq.getAligned().length(); }
188 return alignSeqs.size();
190 catch(exception& e) {
191 errorOut(e, "PreClusterCommand", "readSeqs");
195 /**************************************************************************************************/
196 void PreClusterCommand::readNameFile(){
199 openInputFile(namefile, in);
200 string firstCol, secondCol;
203 in >> firstCol >> secondCol; gobble(in);
204 names[firstCol] = secondCol;
206 while (secondCol.find_first_of(',') != -1) {
208 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
210 sizes[firstCol] = size;
214 catch(exception& e) {
215 errorOut(e, "PreClusterCommand", "readNameFile");
219 /**************************************************************************************************/
220 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
224 for (int i = 0; i < seq1.length(); i++) {
226 if (seq1[i] != seq2[i]) { numBad++; }
227 if (numBad > diffs) { return length; } //to far to cluster
232 catch(exception& e) {
233 errorOut(e, "PreClusterCommand", "calcMisMatches");
237 /**************************************************************************************************/
238 void PreClusterCommand::printData(string newfasta, string newname){
242 openOutputFile(newfasta, outFasta);
243 openOutputFile(newname, outNames);
245 map<string, string>::iterator itNames;
247 for (int i = 0; i < alignSeqs.size(); i++) {
248 if (alignSeqs[i].numIdentical != 0) {
249 alignSeqs[i].seq.printSequence(outFasta);
251 itNames = names.find(alignSeqs[i].seq.getName());
253 outNames << itNames->first << '\t' << itNames->second << endl;
261 catch(exception& e) {
262 errorOut(e, "PreClusterCommand", "printData");
267 /**************************************************************************************************/