//**********************************************************************************************************************
vector<string> BinSeqCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- 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 plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string BinSeqCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The bin.seqs command parameters are list, fasta, name, label and group. The fasta and list are required, unless you have a valid current list and fasta file.\n";
+ helpString += "The bin.seqs command parameters are list, fasta, name, count, label and group. The fasta and list are required, unless you have a valid current list and fasta file.\n";
helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
helpString += "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n";
helpString += "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n";
}
}
//**********************************************************************************************************************
+string BinSeqCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],[distance],fasta"; } //makes file like: amazon.0.03.fasta
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(){
try {
abort = true; calledHelp = true;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //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["count"] = inputDir + it->second; }
+ }
}
else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not found") {
else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (listfile == "not open") { listfile = ""; abort = true; }
+ else { m->setListFile(listfile); }
//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"){
}
namesfile = validParameter.validFile(parameters, "name", true);
- if (namesfile == "not open") { abort = true; }
+ if (namesfile == "not open") { namesfile = ""; abort = true; }
else if (namesfile == "not found") { namesfile = ""; }
+ else { m->setNameFile(namesfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namesfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
+ if (countfile == "") {
+ if (namesfile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
fasta->readFastaFile(fastafile);
//if user gave a namesfile then use it
- if (namesfile != "") {
- readNamesFile();
- }
+ if (namesfile != "") { readNamesFile(); }
+ if (countfile != "") { ct.readTable(countfile); }
input = new InputData(listfile, "list");
list = input->getListVector();
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector();
}
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
delete list;
}
delete fasta;
if (groupfile != "") { delete groupMap; }
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
-
- delete input;
- delete fasta;
- if (groupfile != "") { delete groupMap; }
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //set align file as new current fastafile
+ string currentFasta = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
//return 1 if error, 0 otherwise
int BinSeqCommand::process(ListVector* list) {
try {
- string binnames, name, sequence;
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
- m->openOutputFile(outputFileName, out);
-
- //save to output list of output file names
- outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
-
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- //for each bin in the list vector
- for (int i = 0; i < list->size(); i++) {
-
- if (m->control_pressed) { return 1; }
-
- binnames = list->get(i);
- while (binnames.find_first_of(',') != -1) {
- name = binnames.substr(0,binnames.find_first_of(','));
- binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-
- //do work for that name
- sequence = fasta->getSequence(name);
- if (sequence != "not found") {
- //if you don't have groups
- if (groupfile == "") {
- name = name + "\t" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }else {//if you do have groups
- string group = groupMap->getGroup(name);
- if (group == "not found") {
- m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }else{
- name = name + "\t" + group + "\t" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }
- }
- }else {
- m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }
-
- }
-
- //get last name
- sequence = fasta->getSequence(binnames);
- if (sequence != "not found") {
- //if you don't have groups
- if (groupfile == "") {
- binnames = binnames + "\t" + toString(i+1);
- out << ">" << binnames << endl;
- out << sequence << endl;
- }else {//if you do have groups
- string group = groupMap->getGroup(binnames);
- if (group == "not found") {
- m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }else{
- binnames = binnames + "\t" + group + "\t" + toString(i+1);
- out << ">" << binnames << endl;
- out << sequence << endl;
- }
- }
- }else {
- m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }
- }
-
- out.close();
- return 0;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = list->getLabel();
+ string outputFileName = getOutputFileName("fasta", variables);
+
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->size(); i++) {
+
+ if (m->control_pressed) { return 1; }
+
+ string binnames = list->get(i);
+ vector<string> names;
+ m->splitAtComma(binnames, names);
+ for (int j = 0; j < names.size(); j++) {
+ string name = names[j];
+
+ //do work for that name
+ string sequence = fasta->getSequence(name);
+
+ if (countfile != "") {
+ if (sequence != "not found") {
+ if (ct.hasGroupInfo()) {
+ vector<string> groups = ct.getGroups(name);
+ string groupInfo = "";
+ for (int k = 0; k < groups.size()-1; k++) {
+ groupInfo += groups[k] + "-";
+ }
+ if (groups.size() != 0) { groupInfo += groups[groups.size()-1]; }
+ else { groupInfo = "not found"; }
+ name = name + "\t" + groupInfo + "\t" + toString(i+1)+ "\tNumRep=" + toString(ct.getNumSeqs(name));
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }else {
+ name = name + "\t" + toString(i+1) + "\tNumRep=" + toString(ct.getNumSeqs(name));
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }
+
+ }else { m->mothurOut(name + " is missing from your fasta. Does your list file contain all sequence names or just the uniques?"); m->mothurOutEndLine(); return 1; }
+ }else {
+ if (sequence != "not found") {
+ //if you don't have groups
+ if (groupfile == "") {
+ name = name + "\t" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(name);
+ if (group == "not found") {
+ m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }else{
+ name = name + "\t" + group + "\t" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }
+ }
+ }else { m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine(); return 1; }
+ }
+ }
+ }
+
+ out.close();
+ return 0;
}
catch(exception& e) {
projects / mothur.git / blobdiff