A78254471164D7790002E2DD /* chimerapintailcommand.cpp */,
A747E81C116365E000FB9042 /* chimeraslayercommand.h */,
A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */,
- A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
A7DA201E113FECD400BF472F /* classifyseqscommand.h */,
+ A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
A7DA2021113FECD400BF472F /* clustercommand.cpp */,
A7DA2022113FECD400BF472F /* clustercommand.h */,
A7DA2025113FECD400BF472F /* collectcommand.cpp */,
A7DA2063113FECD400BF472F /* getrabundcommand.h */,
A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
A7DA2065113FECD400BF472F /* getsabundcommand.h */,
- A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
A7DA2067113FECD400BF472F /* getseqscommand.h */,
+ A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
A7DA2069113FECD400BF472F /* getsharedotucommand.h */,
A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
//delete inFileName;
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; }
-
- if(namefile != "") { MPIReadNamesFile(namefileNames[s]); }
if (pid == 0) { //you are the root process
MPI_File_close(&outMPITempTax);
#else
- //read namefile
- if(namefile != "") {
- nameMap.clear(); //remove old names
-
- ifstream inNames;
- openInputFile(namefileNames[s], inNames);
-
- string firstCol, secondCol;
- while(!inNames.eof()) {
- inNames >> firstCol >> secondCol; gobble(inNames);
- nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
- }
- inNames.close();
- }
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
ifstream inFASTA;
openInputFile(fastaFileNames[s], inFASTA);
#ifdef USE_MPI
if (pid == 0) { //this part does not need to be paralellized
+
+ if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush(); MPIReadNamesFile(namefileNames[s]); m->mothurOut(" Done."); m->mothurOutEndLine(); }
+ #else
+ //read namefile
+ if(namefile != "") {
+
+ m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
+
+ nameMap.clear(); //remove old names
+
+ ifstream inNames;
+ openInputFile(namefileNames[s], inNames);
+
+ string firstCol, secondCol;
+ while(!inNames.eof()) {
+ inNames >> firstCol >> secondCol; gobble(inNames);
+
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+
+ nameMap[firstCol] = temp;
+ }
+ inNames.close();
+
+ m->mothurOut(" Done."); m->mothurOutEndLine();
+ }
#endif
m->mothurOutEndLine();
PhyloSummary taxaSum(taxonomyFileName, group);
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; }
-
+
if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); }
else {
ifstream in;
//read in users taxonomy file and add sequences to tree
string name, taxon;
+
while(!in.eof()){
in >> name >> taxon; gobble(in);
if (itNames == nameMap.end()) {
m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
}else{
- for (int i = 0; i < itNames->second; i++) {
- taxaSum.addSeqToTree(name, taxon); //add it as many times as there are identical seqs
+ for (int i = 0; i < itNames->second.size(); i++) {
+ taxaSum.addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
}
+ itNames->second.clear();
+ nameMap.erase(itNames->first);
}
}
in.close();
string firstCol, secondCol;
while(!iss.eof()) {
iss >> firstCol >> secondCol; gobble(iss);
- nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
+
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+
+ nameMap[firstCol] = temp;
}
MPI_File_close(&inMPI);
vector<string> fastaFileNames;
vector<string> namefileNames;
vector<string> groupfileNames;
- map<string, int> nameMap;
- map<string, int>::iterator itNames;
+ map<string, vector<string> > nameMap;
+ map<string, vector<string> >::iterator itNames;
Classify* classify;
#include "chimerabellerophoncommand.h"
#include "setlogfilecommand.h"
#include "phylodiversitycommand.h"
+#include "makegroupcommand.h"
/*******************************************************/
commands["parse.sff"] = "parse.sff";
commands["set.logfile"] = "set.logfile";
commands["phylo.diversity"] = "phylo.diversity";
+ commands["make.group"] = "make.group";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
else if(commandName == "parse.list") { command = new ParseListCommand(optionString); }
else if(commandName == "parse.sff") { command = new ParseSFFCommand(optionString); }
else if(commandName == "phylo.diversity") { command = new PhyloDiversityCommand(optionString); }
+ else if(commandName == "make.group") { command = new MakeGroupCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
./fileoutput.o\\r
./globaldata.o\\r
./groupmap.o\\r
- ./helpcommand.o\\r
+ ./helpcommand.o\
+ ./makegroupcommand.o\\r
./inputdata.o\\r
./jackknife.o\\r
./kmer.o\\r
./fileoutput.o\\r
./globaldata.o\\r
./groupmap.o\\r
- ./helpcommand.o\\r
+ ./helpcommand.o\
+ ./makegroupcommand.o\\r
./inputdata.o\\r
./jackknife.o\\r
./kmer.o\\r
./logsd.o\\r
./geom.o\
./setlogfilecommand.o\\r
- -o mothur\r
+ -o ../Release/mothur\r
\r
clean : \r
rm \\r
./fileoutput.o\\r
./globaldata.o\\r
./groupmap.o\\r
- ./helpcommand.o\\r
+ ./helpcommand.o\
+ ./makegroupcommand.o\\r
./inputdata.o\\r
./jackknife.o\\r
./kmer.o\\r
./phylodiversitycommand.o : phylodiversitycommand.cpp\r
$(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o\r
\r
+# Item # 201 -- makegroupcommand --\r
+./makegroupcommand.o : makegroupcommand.cpp\r
+ $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o\r
\r
\r
##### END RUN ####\r
*/
#include "makegroupcommand.h"
+#include "sequence.hpp"
//**********************************************************************************************************************
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
+ filename = outputDir;
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; }
in.close();
if (ableToOpen == 1) {
- m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
- }
+ }else{ filename += getRootName(getSimpleName(fastaFileNames[i])); }
}
+ filename += "groups";
+
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
-
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
+ else { splitAtDash(groups, groupsNames); }
+
+ if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true; }
}
}
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");
+ m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
+ m->mothurOut("The make.group command parameters are fasta and groups, both are required.\n");
+ m->mothurOut("The make.group command should be in the following format: \n");
+ m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups. \n");
+ m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "help");
try {
if (abort == true) { return 0; }
+ ofstream out;
+ openOutputFile(filename, out);
+
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+
+ ifstream in;
+ openInputFile(fastaFileNames[i], in);
+
+ while (!in.eof()) {
+
+ Sequence seq(in); gobble(in);
+
+ if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; }
+ }
+ in.close();
+ }
+
+ out.close();
m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- //for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
exit(1);
}
}
+//**********************************************************************************************************************
+
private:
- string fastaFileName, groups, outputDir;
+ string fastaFileName, groups, outputDir, filename;
vector<string> fastaFileNames;
vector<string> groupsNames;
projects / mothur.git / commitdiff