#include "listvector.hpp"
//**********************************************************************************************************************
-vector<string> RemoveSeqsCommand::getValidParameters(){
+vector<string> RemoveSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta","name", "group", "alignreport", "accnos", "qfile","list","taxonomy","outputdir","inputdir", "dups" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
+ 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); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "getValidParameters");
+ m->errorOut(e, "RemoveSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-RemoveSeqsCommand::RemoveSeqsCommand(){
+string RemoveSeqsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["taxonomy"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["alignreport"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
+ string helpString = "";
+ helpString += "The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n";
+ helpString += "It outputs a file containing the sequences NOT in the .accnos file.\n";
+ helpString += "The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos and at least one of the file parameters.\n";
+ helpString += "The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n";
+ helpString += "The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
+ helpString += "Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
+ m->errorOut(e, "RemoveSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> RemoveSeqsCommand::getRequiredParameters(){
+string RemoveSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
try {
- string Array[] = {"accnos"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "qfile") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "alignreport") { outputFileName = "pick.align.report"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
}
catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "getRequiredParameters");
+ m->errorOut(e, "RemoveSeqsCommand", "getOutputFileNameTag");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> RemoveSeqsCommand::getRequiredFiles(){
+RemoveSeqsCommand::RemoveSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
exit(1);
}
}
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport", "accnos", "qfile", "list","taxonomy","outputdir","inputdir", "dups" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "not open") { abort = true; }
- else if (accnosfile == "not found") { accnosfile = ""; m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }
+ else if (accnosfile == "not found") {
+ accnosfile = m->getAccnosFile();
+ if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setAccnosFile(accnosfile); }
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
+ if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
-
+ else { m->setFastaFile(fastafile); }
+
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
-
+ else { m->setNameFile(namefile); }
+
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
alignfile = validParameter.validFile(parameters, "alignreport", true);
if (alignfile == "not open") { abort = true; }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not open") { abort = true; }
else if (taxfile == "not found") { taxfile = ""; }
+ else { m->setTaxonomyFile(taxfile); }
qualfile = validParameter.validFile(parameters, "qfile", true);
if (qualfile == "not open") { abort = true; }
else if (qualfile == "not found") { qualfile = ""; }
-
+ else { m->setQualFile(qualfile); }
string usedDups = "true";
string temp = validParameter.validFile(parameters, "dups", false);
if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; }
- if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
+ if ((fastafile != "") && (namefile == "")) {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
}
//**********************************************************************************************************************
-void RemoveSeqsCommand::help(){
- try {
- m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n");
- m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
- m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos and at least one of the file parameters.\n");
- m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n");
- m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
- m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int RemoveSeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
- readAccnos();
+ names = m->readAccnos(accnosfile);
if (m->control_pressed) { return 0; }
if (taxfile != "") { readTax(); }
if (qualfile != "") { readQual(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
-
- m->mothurOut("Removed " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
-
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
if (outputNames.size() != 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();
+
+ //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); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ itTypes = outputTypes.find("taxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+ }
+
+ itTypes = outputTypes.find("qfile");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+ }
}
return 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
ofstream out;
m->openOutputFile(outputFileName, out);
string name;
bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
wroteSomething = true;
currSeq.printSequence(out);
- }
+ }else { removedCount++; }
}
m->gobble(in);
}
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
+
return 0;
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" + m->getExtension(qualfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
ofstream out;
m->openOutputFile(outputFileName, out);
string name;
bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
wroteSomething = true;
out << name << endl << scores;
- }
+ }else { removedCount++; }
m->gobble(in);
}
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your quality file."); m->mothurOutEndLine();
+
return 0;
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
ofstream out;
m->openOutputFile(outputFileName, out);
m->openInputFile(listfile, in);
bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
+
+ removedCount = 0;
+
//read in list vector
ListVector list(in);
//for each bin
for (int i = 0; i < list.getNumBins(); i++) {
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
//parse out names that are in accnos file
string binnames = list.get(i);
//if that name is in the .accnos file, add it
if (names.count(name) == 0) { newNames += name + ","; }
+ else { removedCount++; }
}
//get last name
if (names.count(binnames) == 0) { newNames += binnames + ","; }
+ else { removedCount++; }
//if there are names in this bin add to new list
if (newNames != "") {
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
+
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
+
return 0;
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
ofstream out;
m->openOutputFile(outputFileName, out);
string name, firstCol, secondCol;
bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
-
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
in >> firstCol; m->gobble(in);
in >> secondCol;
-
+
vector<string> parsedNames;
- //parse second column saving each name
- while (secondCol.find_first_of(',') != -1) {
- name = secondCol.substr(0,secondCol.find_first_of(','));
- secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
- parsedNames.push_back(name);
- }
+ m->splitAtComma(secondCol, parsedNames);
- //get name after last ,
- parsedNames.push_back(secondCol);
-
vector<string> validSecond; validSecond.clear();
for (int i = 0; i < parsedNames.size(); i++) {
if (names.count(parsedNames[i]) == 0) {
if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone
for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
+ removedCount += parsedNames.size();
}else {
- //if the name in the first column is in the set then print it and any other names in second column also in set
+ removedCount += parsedNames.size()-validSecond.size();
+ //if the name in the first column is in the set then print it and any other names in second column also in set
if (names.count(firstCol) == 0) {
wroteSomething = true;
}
in.close();
out.close();
-
+
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
+
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
ofstream out;
m->openOutputFile(outputFileName, out);
string name, group;
bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
in >> group; //read from second column
if (names.count(name) == 0) {
wroteSomething = true;
out << name << '\t' << group << endl;
- }
+ }else { removedCount++; }
m->gobble(in);
}
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine();
+
+
return 0;
}
catch(exception& e) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
ofstream out;
m->openOutputFile(outputFileName, out);
string name, tax;
bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
in >> tax; //read from second column
if (names.count(name) == 0) {
wroteSomething = true;
out << name << '\t' << tax << endl;
- }
+ }else { removedCount++; }
m->gobble(in);
}
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
ofstream out;
m->openOutputFile(outputFileName, out);
string name, junk;
bool wroteSomething = false;
+ int removedCount = 0;
//read column headers
for (int i = 0; i < 16; i++) {
out << endl;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
out << endl;
}else {//still read just don't do anything with it
+ removedCount++;
//read rest
for (int i = 0; i < 15; i++) {
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["alignreport"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
+
+
return 0;
}
}
}
//**********************************************************************************************************************
-void RemoveSeqsCommand::readAccnos(){
- try {
-
- ifstream in;
- m->openInputFile(accnosfile, in);
- string name;
-
- while(!in.eof()){
- in >> name;
-
- names.insert(name);
-
- m->gobble(in);
- }
- in.close();
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "readAccnos");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
projects / mothur.git / blobdiff