+++ /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);
- }
-}
-//**********************************************************************************************************************
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