--- /dev/null
+/*
+ * listseqscommand.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 7/8/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "listseqscommand.h"
+#include "sequence.hpp"
+#include "listvector.hpp"
+
+
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",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, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+ helpString += "The list.seqs command parameters are fasta, name, group, 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);
+ }
+}
+
+//**********************************************************************************************************************
+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) {
+ try {
+ abort = false; calledHelp = false;
+
+ //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();
+
+ 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; }
+ }
+ }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ 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, "alignreport", true);
+ if (alignfile == "not open") { abort = true; }
+ else if (alignfile == "not found") { alignfile = ""; }
+
+ 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); }
+
+ if ((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() > okay) { m->mothurOut("You may only enter one file."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ListSeqsCommand::execute(){
+ try {
+
+ 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(); }
+
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
+
+ //sort in alphabetical order
+ sort(names.begin(), names.end());
+
+ if (outputDir == "") { outputDir += m->hasPath(inputFileName); }
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + "accnos";
+
+ ofstream 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 Name: "); 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) {
+ m->errorOut(e, "ListSeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int ListSeqsCommand::readFasta(){
+ try {
+
+ ifstream 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();
+ //if (lastName == "") { lastName = name; }
+ //if (name != lastName) { count = 1; }
+ // lastName = name;
+
+ //Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
+ //newSeq.printSequence(out);
+
+ if (name != "") { names.push_back(name); }
+
+ m->gobble(in);
+ //count++;
+ }
+ in.close();
+ //out.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ 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);
+ }
+}
+
+//**********************************************************************************************************************
+int ListSeqsCommand::readName(){
+ try {
+
+ ifstream 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
+ m->splitAtComma(secondCol, names);
+
+ m->gobble(in);
+ }
+ in.close();
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "readName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int ListSeqsCommand::readGroup(){
+ try {
+
+ ifstream in;
+ m->openInputFile(groupfile, in);
+ string name, group;
+
+ while(!in.eof()){
+
+ 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);
+
+ m->gobble(in);
+ }
+ in.close();
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "readGroup");
+ 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
+int ListSeqsCommand::readAlign(){
+ try {
+
+ ifstream in;
+ m->openInputFile(alignfile, in);
+ string name, junk;
+
+ //read column headers
+ for (int i = 0; i < 16; i++) {
+ 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; }
+ else { break; }
+ }
+
+ names.push_back(name);
+
+ 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) {
+ m->errorOut(e, "ListSeqsCommand", "readTax");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff