*/
#include "preclustercommand.h"
+#include "sequenceparser.h"
+#include "deconvolutecommand.h"
//**********************************************************************************************************************
inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); }
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 pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
+ CommandParameter pbygroup("bygroup", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pbygroup);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
helpString += "The pre.cluster command outputs a new fasta and name file.\n";
helpString += "The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \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 group parameter allows you to provide a group file. \n";
helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
+ helpString += "The bygroup parameter allows you to indicate you whether you want to cluster sequences only within each group, default=T, when a groupfile is given. \n";
helpString += "The pre.cluster command should be in the following format: \n";
helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
}
//check for required parameters
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not found") { namefile = ""; }
else if (namefile == "not open") { abort = true; }
- else { readNameFile(); m->setNameFile(namefile); }
+ else { m->setNameFile(namefile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not found") { groupfile = ""; }
+ else if (groupfile == "not open") { abort = true; groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
- string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
+ string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
convert(temp, diffs);
+
+ temp = validParameter.validFile(parameters, "bygroup", false);
+ if (temp == "not found") {
+ if (groupfile != "") { temp = "T"; }
+ else { temp = "F"; }
+ }
+ bygroup = m->isTrue(temp);
+
+ if (bygroup && (groupfile == "")) { m->mothurOut("You cannot set bygroup=T, unless you provide a groupfile."); m->mothurOutEndLine(); abort=true; }
+
}
}
int start = time(NULL);
- //reads fasta file and return number of seqs
- int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
+ string newNamesFile = fileroot + "precluster.names";
- 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; }
+ if (bygroup) {
+ //clear out old files
+ ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
+ ofstream outNames; m->openOutputFile(newNamesFile, outNames); outNames.close();
+
+ //parse fasta and name file by group
+ SequenceParser* parser;
+ if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile); }
+ else { parser = new SequenceParser(groupfile, fastafile); }
+
+ vector<string> groups = parser->getNamesOfGroups();
+
+ //precluster each group
+ for (int i = 0; i < groups.size(); i++) {
+
+ start = time(NULL);
+
+ if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
+
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
+
+ map<string, string> thisNameMap;
+ if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
+ vector<Sequence> thisSeqs = parser->getSeqs(groups[i]);
+
+ //fill alignSeqs with this groups info.
+ int numSeqs = loadSeqs(thisNameMap, thisSeqs);
+
+ if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
+
+ if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; }
+
+ int count = process();
+
+ if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
+
+ m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+ m->mothurOut("pre.cluster 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();
+
+ }
+
+ //run unique.seqs for deconvolute results
+ string inputString = "fasta=" + newFastaFile;
+ if (namefile != "") { inputString += ", name=" + newNamesFile; }
+ m->mothurOutEndLine();
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
+
+ Command* uniqueCommand = new DeconvoluteCommand(inputString);
+ uniqueCommand->execute();
+
+ map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
+
+ delete uniqueCommand;
+
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ newNamesFile = filenames["name"][0];
+ newFastaFile = filenames["fasta"][0];
+
+ }else {
+ if (namefile != "") { readNameFile(); }
+
+ //reads fasta file and return number of seqs
+ 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; }
+
+ int count = process();
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+ m->mothurOut("pre.cluster 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(); outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
+ m->mothurOut(newNamesFile); m->mothurOutEndLine(); outputNames.push_back(newNamesFile); 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, "PreClusterCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int PreClusterCommand::process(){
+ try {
+
//sort seqs by number of identical seqs
sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
-
+
int count = 0;
-
+ int numSeqs = alignSeqs.size();
+
//think about running through twice...
for (int i = 0; i < numSeqs; i++) {
//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
+
+ //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 + "precluster" + m->getExtension(fastafile);
- string newNamesFile = fileroot + "precluster.names";
-
- if (m->control_pressed) { return 0; }
-
- m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
- m->mothurOut("pre.cluster 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(); outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
- m->mothurOut(newNamesFile); m->mothurOutEndLine(); outputNames.push_back(newNamesFile); 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); }
- }
+ if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
- return 0;
+ return count;
}
catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "execute");
+ m->errorOut(e, "PreClusterCommand", "process");
exit(1);
}
}
-
/**************************************************************************************************/
-
-//this requires the names and fasta file to be in the same order
-
int PreClusterCommand::readFASTA(){
try {
//ifstream inNames;
exit(1);
}
}
-
+/**************************************************************************************************/
+int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
+ try {
+ length = 0;
+ alignSeqs.clear();
+ map<string, string>::iterator it;
+ bool error = false;
+
+ for (int i = 0; i < thisSeqs.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ if (namefile != "") {
+ it = thisName.find(thisSeqs[i].getName());
+
+ //should never be true since parser checks for this
+ if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
+ else{
+ //get number of reps
+ int numReps = 0;
+ for(int j=0;j<(it->second).length();j++){
+ if((it->second)[j] == ','){ numReps++; }
+ }
+
+ seqPNode tempNode(numReps, thisSeqs[i], it->second);
+ alignSeqs.push_back(tempNode);
+ if (thisSeqs[i].getAligned().length() > length) { length = thisSeqs[i].getAligned().length(); }
+ }
+ }else { //no names file, you are identical to yourself
+ seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
+ alignSeqs.push_back(tempNode);
+ if (thisSeqs[i].getAligned().length() > length) { length = thisSeqs[i].getAligned().length(); }
+ }
+ }
+
+ //sanity check
+ if (error) { m->control_pressed = true; }
+
+ thisSeqs.clear();
+
+ return alignSeqs.size();
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "loadSeqs");
+ exit(1);
+ }
+}
+
/**************************************************************************************************/
int PreClusterCommand::calcMisMatches(string seq1, string seq2){
ofstream outFasta;
ofstream outNames;
- m->openOutputFile(newfasta, outFasta);
- m->openOutputFile(newname, outNames);
+ if (bygroup) {
+ m->openOutputFileAppend(newfasta, outFasta);
+ m->openOutputFileAppend(newname, outNames);
+ }else {
+ 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);
projects / mothur.git / blobdiff