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A7DA207F113FECD400BF472F /* helpcommand.h */,
A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
A7DA208E113FECD400BF472F /* libshuffcommand.h */,
- A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
A7DA2090113FECD400BF472F /* listseqscommand.h */,
+ A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
+ A703FE931194645F002C397E /* makegroupcommand.h */,
+ A703FE941194645F002C397E /* makegroupcommand.cpp */,
A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
--- /dev/null
+/*
+ * makegroupcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/7/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "makegroupcommand.h"
+
+//**********************************************************************************************************************
+
+MakeGroupCommand::MakeGroupCommand(string option) {
+ try {
+
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+
+ //valid paramters for this command
+ string AlignArray[] = {"fasta","groups","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //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 = ""; }
+
+
+ //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 = ""; }
+
+
+ fastaFileName = validParameter.validFile(parameters, "fasta", false);
+ if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(fastaFileName, fastaFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = openInputFile(fastaFileNames[i], in);
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }
+
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+MakeGroupCommand::~MakeGroupCommand(){ }
+
+//**********************************************************************************************************************
+
+void MakeGroupCommand::help(){
+ try {
+ m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
+ m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
+ m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
+ m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
+ m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
+ m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
+ m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
+ m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
+ m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
+ m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
+ m->mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.\n");
+ m->mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");
+ m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
+ m->mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
+ m->mothurOut("The align.seqs command should be in the following format: \n");
+ m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
+ m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "help");
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+
+int MakeGroupCommand::execute(){
+ try {
+ if (abort == true) { return 0; }
+
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ //for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "execute");
+ exit(1);
+ }
+}
+
--- /dev/null
+#ifndef MAKEGROUPCOMMAND_H
+#define MAKEGROUPCOMMAND_H
+
+/*
+ * makegroupcommand.h
+ * Mothur
+ *
+ * Created by westcott on 5/7/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class MakeGroupCommand : public Command {
+
+public:
+ MakeGroupCommand(string);
+ ~MakeGroupCommand();
+ int execute();
+ void help();
+
+private:
+
+ string fastaFileName, groups, outputDir;
+ vector<string> fastaFileNames;
+ vector<string> groupsNames;
+
+ bool abort;
+};
+
+#endif
+
else {
//valid paramters for this command
string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
- "qthreshold", "qaverage", "allfiles", "qtrim","diffs", "processors", "outputdir","inputdir"};
+ "qthreshold", "qaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
convert(temp, maxLength);
- temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found") { temp = "0"; }
- convert(temp, diffs);
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, tdiffs);
+
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, pdiffs);
temp = validParameter.validFile(parameters, "qfile", true);
if (temp == "not found") { qFileName = ""; }
m->mothurOut("The maxhomop parameter .... The default is 0.\n");
m->mothurOut("The minlength parameter .... The default is 0.\n");
m->mothurOut("The maxlength parameter .... The default is 0.\n");
- m->mothurOut("The diffs parameter .... The default is 0.\n");
+ m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is 0.\n");
+ m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
+ m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
m->mothurOut("The qfile parameter .....\n");
m->mothurOut("The qthreshold parameter .... The default is 0.\n");
m->mothurOut("The qaverage parameter .... The default is 0.\n");
if (origSeq != "") {
int group;
string trashCode = "";
+ int currentSeqsDiffs = 0;
if(qFileName != ""){
if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
if(barcodes.size() != 0){
success = stripBarcode(currSeq, group);
if(!success){ trashCode += 'b'; }
+ else{ currentSeqsDiffs += currentSeqsTdiffs; }
}
if(numFPrimers != 0){
success = stripForward(currSeq);
if(!success){ trashCode += 'f'; }
+ else{ currentSeqsDiffs += currentSeqsTdiffs; }
}
-
+
+ if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
+
if(numRPrimers != 0){
success = stripReverse(currSeq);
if(!success){ trashCode += 'r'; }
}
//if you found the barcode or if you don't want to allow for diffs
- if ((diffs == 0) || (success == 1)) { return success; }
+ if ((bdiffs == 0) || (success == 1)) { return success; }
else { //try aligning and see if you can find it
map<string,int>::iterator it=barcodes.begin();
string temp = it->first;
- alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (temp.length()+diffs+1));
+ alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (temp.length()+bdiffs+1));
}else{ alignment = NULL; }
}
//use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,length+diffs));
+ alignment->align(oligo, rawSequence.substr(0,length+bdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
//cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,oligo.length()) << " raw aligned = " << temp << endl;
int newStart=0;
- if(compareDNASeq(oligo, temp, length, newStart)){
+ if(compareDNASeq(oligo, temp, length, newStart, bdiffs)){
group = it->second;
seq.setUnaligned(rawSequence.substr(newStart));
success = 1;
}
//if you found the primer or if you don't want to allow for diffs
- if ((diffs == 0) || (success == 1)) { return success; }
+ if ((pdiffs == 0) || (success == 1)) { return success; }
else { //try aligning and see if you can find it
-
Alignment* alignment;
- if (numFPrimers > 0) { alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (forPrimer[0].length()+diffs+1)); } //assumes primers are all the same length
+ if (numFPrimers > 0) { alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (forPrimer[0].length()+pdiffs+1)); }
else{ alignment = NULL; }
-
//can you find the primer
for(int i=0;i<numFPrimers;i++){
string oligo = forPrimer[i];
int length = oligo.length();
-
+
if(rawSequence.length() < oligo.length()){
success = 0;
break;
}
+
+ //resize if neccessary
+ if ((length+pdiffs+1) > alignment->getnRows()) { alignment->resize(length+pdiffs+1); }
//use needleman to align first primer.length()+numdiffs of sequence to each primer
- alignment->align(oligo, rawSequence.substr(0,length+diffs));
+ alignment->align(oligo, rawSequence.substr(0,length+pdiffs));
oligo = alignment->getSeqAAln();
string temp = alignment->getSeqBAln();
-
+
int newStart = 0;
- if(compareDNASeq(oligo, temp, length, newStart)){
+ if(compareDNASeq(oligo, temp, length, newStart, pdiffs)){
seq.setUnaligned(rawSequence.substr(newStart));
success = 1;
break;
}
//***************************************************************************************************************
-bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int& end){
+bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int& end, int diffs){
try {
bool success = 1;
int length = oligo.length();
- end = length;
+ end = numBases;
int countBases = 0;
int countDiffs = 0;
if (length != 0) {
- if ((oligo[0] == '-') || (oligo[0] == '.')) { success = 0; return success; } //no gaps allowed at beginning
+ if ((oligo[0] == '-') || (oligo[0] == '.')) { success = 0; return success; } //no gaps allowed at beginning
}
for(int i=0;i<length;i++){
if ((oligo[i] != '-') && (oligo[i] != '.')) { countBases++; }
-
- //cout << oligo[i] << " " << seq[i] << " diffs = " << countDiffs << " countBases = " << countBases << endl;
-
+
if(oligo[i] != seq[i]){
if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.') { countDiffs++; }
else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { countDiffs++; }
success = 1;
}
- if (countBases >= numBases) { end = i; break; } //stop checking after end of barcode or primer
+ if (countBases >= numBases) { end = countBases; break; } //stop checking after end of barcode or primer
}
-
+
+ //if it's a success we want to check for total diffs in driver, so save it.
+ if (success == 1) { currentSeqsTdiffs = countDiffs; }
+
return success;
}
catch(exception& e) {
bool cullHomoP(Sequence&);
bool cullAmbigs(Sequence&);
bool compareDNASeq(string, string);
- bool compareDNASeq(string, string, int, int&);
+ bool compareDNASeq(string, string, int, int&, int);
bool abort;
string fastaFile, oligoFile, qFileName, outputDir;
bool flip, allFiles, qtrim;
- int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, diffs;
+ int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, currentSeqsTdiffs;
vector<string> forPrimer, revPrimer, outputNames;
map<string, int> barcodes;
vector<string> groupVector;
projects / mothur.git / commitdiff