#include "listseqscommand.h"
#include "sequence.hpp"
+#include "listvector.hpp"
+#include "counttable.h"
+
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false); parameters.push_back(palignreport);
+ 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, "ListSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ListSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The list.seqs command reads a fasta, name, group, count, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+ helpString += "The list.seqs command parameters are fasta, name, group, count, list, taxonomy and alignreport. You must provide one of these parameters.\n";
+ helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
+ helpString += "Example list.seqs(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, "ListSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ListSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "accnos") { pattern = "[filename],accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ListSeqsCommand::ListSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-ListSeqsCommand::ListSeqsCommand(string option){
+ListSeqsCommand::ListSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
-
+ 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", "align" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+
+ //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 = ""; }
+ else {
+ string path;
+ it = parameters.find("alignreport");
+ //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["alignreport"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //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["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //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["taxonomy"] = 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; }
+ }
+ }
+
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; }
+ else if (fastafile == "not found") { fastafile = ""; }
+ else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { 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 { m->setGroupFile(groupfile); }
- alignfile = validParameter.validFile(parameters, "align", true);
+ alignfile = validParameter.validFile(parameters, "alignreport", true);
if (alignfile == "not open") { abort = true; }
else if (alignfile == "not found") { alignfile = ""; }
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "")) { mothurOut("You must provide a file."); mothurOutEndLine(); 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); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile == "") && (fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == "")) { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
+
+ int okay = 1;
+ if (outputDir != "") { okay++; }
+ if (inputDir != "") { okay++; }
- if (parameters.size() > 1) { mothurOut("You may only enter one file."); mothurOutEndLine(); abort = true; }
+ if (parameters.size() > okay) { m->mothurOut("You may only enter one file."); m->mothurOutEndLine(); abort = true; }
}
}
catch(exception& e) {
- errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void ListSeqsCommand::help(){
- try {
- mothurOut("The list.seqs command reads a fasta, name, group or alignreport file and outputs a .accnos file containing sequence names.\n");
- mothurOut("The list.seqs command parameters are fasta, name, group and align. You must provide one of these parameters.\n");
- mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
- mothurOut("Example list.seqs(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, "ListSeqsCommand", "help");
+ m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
exit(1);
}
}
-
//**********************************************************************************************************************
int ListSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read functions fill names vector
if (fastafile != "") { inputFileName = fastafile; readFasta(); }
else if (namefile != "") { inputFileName = namefile; readName(); }
else if (groupfile != "") { inputFileName = groupfile; readGroup(); }
else if (alignfile != "") { inputFileName = alignfile; readAlign(); }
+ else if (listfile != "") { inputFileName = listfile; readList(); }
+ else if (taxfile != "") { inputFileName = taxfile; readTax(); }
+ else if (countfile != "") { inputFileName = countfile; readCount(); }
+
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
//sort in alphabetical order
sort(names.begin(), names.end());
- string outputFileName = getRootName(inputFileName) + "accnos";
+ if (outputDir == "") { outputDir += m->hasPath(inputFileName); }
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ string outputFileName = getOutputFileName("accnos", variables);
+
ofstream out;
- openOutputFile(outputFileName, out);
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
//output to .accnos file
for (int i = 0; i < names.size(); i++) {
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
out << names[i] << endl;
}
out.close();
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
+
+ m->setAccnosFile(outputFileName);
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ //set accnos file as new current accnosfile
+ string current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
- errorOut(e, "ListSeqsCommand", "execute");
+ m->errorOut(e, "ListSeqsCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
-void ListSeqsCommand::readFasta(){
+int ListSeqsCommand::readFasta(){
try {
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
string name;
+ //ofstream out;
+ //string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+ //m->openOutputFile(newFastaName, out);
+ int count = 1;
+ //string lastName = "";
+
while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
+
Sequence currSeq(in);
name = currSeq.getName();
- names.push_back(name);
+ if (name != "") { names.push_back(name); }
- gobble(in);
+ m->gobble(in);
+ if (m->debug) { count++; cout << "[DEBUG]: count = " + toString(count) + ", name = " + currSeq.getName() + "\n"; }
}
- in.close();
+ in.close();
+ //out.close();
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "ListSeqsCommand", "readFasta");
+ m->errorOut(e, "ListSeqsCommand", "readFasta");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ListSeqsCommand::readList(){
+ try {
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ if(!in.eof()){
+ //read in list vector
+ ListVector list(in);
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+ string binnames = list.get(i);
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ m->splitAtComma(binnames, names);
+ }
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "readList");
exit(1);
}
}
//**********************************************************************************************************************
-void ListSeqsCommand::readName(){
+int ListSeqsCommand::readName(){
try {
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
string name, firstCol, secondCol;
while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
in >> firstCol;
in >> secondCol;
//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());
- names.push_back(name);
- }
+ m->splitAtComma(secondCol, names);
- //get name after last ,
- names.push_back(secondCol);
-
- gobble(in);
+ m->gobble(in);
}
in.close();
+ return 0;
}
catch(exception& e) {
- errorOut(e, "ListSeqsCommand", "readName");
+ m->errorOut(e, "ListSeqsCommand", "readName");
exit(1);
}
}
//**********************************************************************************************************************
-void ListSeqsCommand::readGroup(){
+int ListSeqsCommand::readGroup(){
try {
ifstream in;
- openInputFile(groupfile, in);
+ m->openInputFile(groupfile, in);
string name, group;
while(!in.eof()){
-
- in >> name; //read from first column
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ in >> name; m->gobble(in); //read from first column
in >> group; //read from second column
names.push_back(name);
- gobble(in);
+ m->gobble(in);
}
in.close();
+ return 0;
}
catch(exception& e) {
- errorOut(e, "ListSeqsCommand", "readGroup");
+ m->errorOut(e, "ListSeqsCommand", "readGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ListSeqsCommand::readCount(){
+ try {
+ CountTable ct;
+ ct.readTable(countfile, false);
+
+ if (m->control_pressed) { return 0; }
+
+ names = ct.getNamesOfSeqs();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "readCount");
exit(1);
}
}
-
//**********************************************************************************************************************
//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
-void ListSeqsCommand::readAlign(){
+int ListSeqsCommand::readAlign(){
try {
ifstream in;
- openInputFile(alignfile, in);
+ m->openInputFile(alignfile, in);
string name, junk;
//read column headers
if (!in.eof()) { in >> junk; }
else { break; }
}
-
+ //m->getline(in);
while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
in >> name; //read from first column
-
+ //m->getline(in);
//read rest
for (int i = 0; i < 15; i++) {
if (!in.eof()) { in >> junk; }
names.push_back(name);
- gobble(in);
+ m->gobble(in);
}
in.close();
+
+ return 0;
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "readAlign");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ListSeqsCommand::readTax(){
+ try {
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+ string name, firstCol, secondCol;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
+ in >> firstCol;
+ in >> secondCol;
+
+ names.push_back(firstCol);
+
+ m->gobble(in);
+
+ }
+ in.close();
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "ListSeqsCommand", "readAlign");
+ m->errorOut(e, "ListSeqsCommand", "readTax");
exit(1);
}
}
projects / mothur.git / blobdiff