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37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
+ A70DECD71063D8B40057C03C /* secondarystructurecommand.h */,
+ A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */,
371B30B30FD7EE67000414CA /* screenseqscommand.h */,
371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
372095C2103196D70004D347 /* chimera.cpp in Sources */,
A75B887E104C16860083C454 /* ccode.cpp in Sources */,
A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */,
+ A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
exit(1);
}
}
+
+/************************************************************/
+vector<string> GroupMap::getNamesSeqs(){
+ try {
+
+ vector<string> names;
+
+ for (it = groupmap.begin(); it != groupmap.end(); it++) {
+ names.push_back(it->first);
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ errorOut(e, "GroupMap", "getNamesSeqs");
+ exit(1);
+ }
+}
+/************************************************************/
+
vector<string> namesOfGroups;
map<string, int> groupIndex; //groupname, vectorIndex in namesOfGroups. - used by collectdisplays.
int getNumSeqs() { return groupmap.size(); }
+ vector<string> getNamesSeqs();
private:
ifstream fileHandle;
if (globaldata->getFormat() == "shared") {
shared = new SharedCommand();
- shared->execute();
+ int okay = shared->execute();
delete shared;
+
+ //problem with shared
+ if (okay == 1) {
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
+ globaldata->setSharedFile("");
+ }else{
- //change format to shared to speed up commands
- globaldata->setFormat("sharedfile");
- globaldata->setListFile("");
- globaldata->setGroupFile("");
- globaldata->setSharedFile(getRootName(filename) + "shared");
+ //change format to shared to speed up commands
+ globaldata->setFormat("sharedfile");
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
+ globaldata->setSharedFile(getRootName(filename) + "shared");
+ }
}
return 0;
}
--- /dev/null
+/*
+ * secondarystructurecommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/18/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "secondarystructurecommand.h"
+#include "sequence.hpp"
+
+//**********************************************************************************************************************
+
+AlignCheckCommand::AlignCheckCommand(string option){
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta","map"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //check for required parameters
+ mapfile = validParameter.validFile(parameters, "map", true);
+ if (mapfile == "not open") { abort = true; }
+ else if (mapfile == "not found") { mapfile = ""; mothurOut("You must provide an map file."); mothurOutEndLine(); abort = true; }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true; }
+
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void AlignCheckCommand::help(){
+ try {
+ //mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group or alignreport file.\n");
+ //mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
+ //mothurOut("The remove.seqs command parameters are accnos, fasta, name, group and alignreport. You must provide accnos and one of the other parameters.\n");
+ //mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
+ //mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
+ //mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "AlignCheckCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+int AlignCheckCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ //get secondary structure info.
+ readMap();
+
+
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ errorOut(e, "AlignCheckCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void AlignCheckCommand::readMap(){
+ try {
+
+ structMap.resize(1, 0);
+ ifstream in;
+
+ openInputFile(mapfile, in);
+
+ while(!in.eof()){
+ int position;
+ in >> position;
+ structMap.push_back(position);
+ gobble(in);
+ }
+ in.close();
+
+ seqLength = structMap.size();
+
+
+ //check you make sure is structMap[10] = 380 then structMap[380] = 10.
+ for(int i=0;i<seqLength;i++){
+ if(structMap[i] != 0){
+ if(structMap[structMap[i]] != i){
+ mothurOut("Your map file contains an error: line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); mothurOutEndLine();
+ }
+ }
+ }
+
+
+ }
+ catch(exception& e) {
+ errorOut(e, "AlignCheckCommand", "readFasta");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
--- /dev/null
+#ifndef SECONDARYSTRUCTURECHECKERCOMMAND_H
+#define SECONDARYSTRUCTURECHECKERCOMMAND_H
+
+/*
+ * secondarystructurecommand.h
+ * Mothur
+ *
+ * Created by westcott on 9/18/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+/**************************************************************************************************/
+
+struct statData {
+ int pound;
+ int tilde;
+ int dash;
+ int plus;
+ int equal;
+ int loop;
+ int total;
+ statData() : pound(0), loop(0), tilde(0), dash(0), plus(0), equal(0), total(0) {};
+};
+
+/**************************************************************************************************/
+
+
+class AlignCheckCommand : public Command {
+
+ public:
+
+ AlignCheckCommand(string);
+ ~AlignCheckCommand(){};
+ int execute();
+ void help();
+
+ private:
+ vector<int> structMap;
+ string mapfile, fastafile;
+ bool abort;
+ int seqLength;
+
+ void readMap();
+};
+
+/**************************************************************************************************/
+#endif
+
if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {
mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine();
+ createMisMatchFile();
+
//delete memory
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
delete SharedList;
globaldata->gSharedList = NULL;
- return(0);
+ return 1;
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
exit(1);
}
}
+//**********************************************************************************************************************
+void SharedCommand::createMisMatchFile() {
+ try {
+ ofstream outMisMatch;
+ string outputMisMatchName = getRootName(globaldata->inputFileName);
+
+ //you have sequences in your list file that are not in your group file
+ if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
+ outputMisMatchName += "missing.group";
+ mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+
+ openOutputFile(outputMisMatchName, outMisMatch);
+
+ //go through list and if group returns "not found" output it
+ for (int i = 0; i < SharedList->getNumBins(); i++) {
+
+ string names = SharedList->get(i);
+
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+ string group = groupMap->getGroup(name);
+
+ if(group == "not found") { outMisMatch << name << endl; }
+ }
+
+ //get last name
+ string group = groupMap->getGroup(names);
+ if(group == "not found") { outMisMatch << names << endl; }
+ }
+
+ outMisMatch.close();
+
+
+ }else {//you have sequences in your group file that are not in you list file
+
+ outputMisMatchName += "missing.name";
+ mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+
+ map<string, string> namesInList;
+
+ //go through listfile and get names
+ for (int i = 0; i < SharedList->getNumSeqs(); i++) {
+
+ string names = SharedList->get(i);
+
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+
+ namesInList[name] = name;
+ }
+
+ //get last name
+ namesInList[names] = names;
+ }
+
+ //get names of sequences in groupfile
+ vector<string> seqNames = groupMap->getNamesSeqs();
+
+ map<string, string>::iterator itMatch;
+
+ openOutputFile(outputMisMatchName, outMisMatch);
+
+ //loop through names in seqNames and if they aren't in namesIn list output them
+ for (int i = 0; i < seqNames.size(); i++) {
+
+ itMatch = namesInList.find(seqNames[i]);
+
+ if (itMatch == namesInList.end()) {
+
+ outMisMatch << seqNames[i] << endl;
+ }
+ }
+ outMisMatch.close();
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "SharedCommand", "createMisMatchFile");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
private:
void printSharedData(vector<SharedRAbundVector*>);
+ void createMisMatchFile();
GlobalData* globaldata;
ReadOTUFile* read;
SharedListVector* SharedList;
projects / mothur.git / commitdiff