+++ /dev/null
-/*
- * removeseqscommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 7/8/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "removeseqscommand.h"
-#include "sequence.hpp"
-#include "listvector.hpp"
-
-//**********************************************************************************************************************
-vector<string> RemoveSeqsCommand::setParameters(){
- try {
- 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", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string RemoveSeqsCommand::getHelpString(){
- try {
- 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", "getHelpString");
- exit(1);
- }
-}
-
-
-//**********************************************************************************************************************
-RemoveSeqsCommand::RemoveSeqsCommand(){
- try {
- 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", "RemoveSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-RemoveSeqsCommand::RemoveSeqsCommand(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 (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["taxonomy"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["alignreport"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["qfile"] = 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("accnos");
- //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["accnos"] = 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("qfile");
- //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["qfile"] = inputDir + it->second; }
- }
- }
-
-
- //check for required parameters
- accnosfile = validParameter.validFile(parameters, "accnos", true);
- if (accnosfile == "not open") { 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") { fastafile = ""; abort = true; }
- else if (fastafile == "not found") { fastafile = ""; }
- else { m->setFastaFile(fastafile); }
-
- namefile = validParameter.validFile(parameters, "name", 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 { 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); }
-
- 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 (temp == "not found") {
- if (namefile != "") { temp = "true"; }
- else { temp = "false"; usedDups = ""; }
- }
- dups = m->isTrue(temp);
-
- 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 ((fastafile != "") && (namefile == "")) {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int RemoveSeqsCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- //get names you want to keep
- readAccnos();
-
- if (m->control_pressed) { return 0; }
-
- //read through the correct file and output lines you want to keep
- if (namefile != "") { readName(); }
- if (fastafile != "") { readFasta(); }
- if (groupfile != "") { readGroup(); }
- if (alignfile != "") { readAlign(); }
- if (listfile != "") { readList(); }
- if (taxfile != "") { readTax(); }
- if (qualfile != "") { readQual(); }
-
- 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;
- }
-
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int RemoveSeqsCommand::readFasta(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ifstream in;
- m->openInputFile(fastafile, in);
- string name;
-
- bool wroteSomething = false;
- int removedCount = 0;
-
- while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
-
- Sequence currSeq(in);
- name = currSeq.getName();
-
- if (name != "") {
- //if this name is in the accnos file
- if (names.count(name) == 0) {
- wroteSomething = true;
-
- currSeq.printSequence(out);
- }else { removedCount++; }
- }
- m->gobble(in);
- }
- in.close();
- out.close();
-
- 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;
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "readFasta");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveSeqsCommand::readQual(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" + m->getExtension(qualfile);
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
-
- ifstream in;
- m->openInputFile(qualfile, in);
- string name;
-
- bool wroteSomething = false;
- int removedCount = 0;
-
-
- while(!in.eof()){
- string saveName = "";
- string name = "";
- string scores = "";
-
- in >> name;
-
- if (name.length() != 0) {
- saveName = name.substr(1);
- while (!in.eof()) {
- char c = in.get();
- if (c == 10 || c == 13){ break; }
- else { name += c; }
- }
- m->gobble(in);
- }
-
- while(in){
- char letter= in.get();
- if(letter == '>'){ in.putback(letter); break; }
- else{ scores += letter; }
- }
-
- m->gobble(in);
-
- if (names.count(saveName) == 0) {
- wroteSomething = true;
-
- out << name << endl << scores;
- }else { removedCount++; }
-
- m->gobble(in);
- }
- in.close();
- out.close();
-
-
- 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;
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "readQual");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveSeqsCommand::readList(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ifstream in;
- m->openInputFile(listfile, in);
-
- bool wroteSomething = false;
- int removedCount = 0;
-
- while(!in.eof()){
-
- removedCount = 0;
-
- //read in list vector
- ListVector list(in);
-
- //make a new list vector
- ListVector newList;
- newList.setLabel(list.getLabel());
-
- //for each bin
- for (int i = 0; i < list.getNumBins(); i++) {
- 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);
-
- string newNames = "";
- while (binnames.find_first_of(',') != -1) {
- string name = binnames.substr(0,binnames.find_first_of(','));
- binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-
- //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 != "") {
- newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
- newList.push_back(newNames);
- }
- }
-
- //print new listvector
- if (newList.getNumBins() != 0) {
- wroteSomething = true;
- newList.print(out);
- }
-
- m->gobble(in);
- }
- in.close();
- out.close();
-
- 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;
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "readList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveSeqsCommand::readName(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ifstream in;
- m->openInputFile(namefile, in);
- string name, firstCol, secondCol;
-
- bool wroteSomething = false;
- int removedCount = 0;
-
- while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
-
- in >> firstCol; m->gobble(in);
- in >> secondCol;
-
- vector<string> parsedNames;
- m->splitAtComma(secondCol, parsedNames);
-
- vector<string> validSecond; validSecond.clear();
- for (int i = 0; i < parsedNames.size(); i++) {
- if (names.count(parsedNames[i]) == 0) {
- validSecond.push_back(parsedNames[i]);
- }
- }
-
- 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 {
- 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;
-
- out << firstCol << '\t';
-
- //you know you have at least one valid second since first column is valid
- for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
- out << validSecond[validSecond.size()-1] << endl;
-
- //make first name in set you come to first column and then add the remaining names to second column
- }else {
-
- //you want part of this row
- if (validSecond.size() != 0) {
-
- wroteSomething = true;
-
- out << validSecond[0] << '\t';
-
- //you know you have at least one valid second since first column is valid
- for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
- out << validSecond[validSecond.size()-1] << endl;
- }
- }
- }
- m->gobble(in);
- }
- 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) {
- m->errorOut(e, "RemoveSeqsCommand", "readName");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int RemoveSeqsCommand::readGroup(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ifstream in;
- m->openInputFile(groupfile, in);
- string name, group;
-
- bool wroteSomething = false;
- int removedCount = 0;
-
- while(!in.eof()){
- 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 this name is in the accnos file
- if (names.count(name) == 0) {
- wroteSomething = true;
- out << name << '\t' << group << endl;
- }else { removedCount++; }
-
- m->gobble(in);
- }
- in.close();
- out.close();
-
- 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) {
- m->errorOut(e, "RemoveSeqsCommand", "readGroup");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveSeqsCommand::readTax(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ifstream in;
- m->openInputFile(taxfile, in);
- string name, tax;
-
- bool wroteSomething = false;
- int removedCount = 0;
-
- while(!in.eof()){
- 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 this name is in the accnos file
- if (names.count(name) == 0) {
- wroteSomething = true;
- out << name << '\t' << tax << endl;
- }else { removedCount++; }
-
- m->gobble(in);
- }
- in.close();
- out.close();
-
- 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) {
- m->errorOut(e, "RemoveSeqsCommand", "readTax");
- 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 RemoveSeqsCommand::readAlign(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ifstream in;
- m->openInputFile(alignfile, in);
- string name, junk;
-
- bool wroteSomething = false;
- int removedCount = 0;
-
- //read column headers
- for (int i = 0; i < 16; i++) {
- if (!in.eof()) { in >> junk; out << junk << '\t'; }
- else { break; }
- }
- out << endl;
-
- while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
-
- in >> name; //read from first column
-
- //if this name is in the accnos file
- if (names.count(name) == 0) {
- wroteSomething = true;
-
- out << name << '\t';
-
- //read rest
- for (int i = 0; i < 15; i++) {
- if (!in.eof()) { in >> junk; out << junk << '\t'; }
- else { break; }
- }
- out << endl;
-
- }else {//still read just don't do anything with it
- removedCount++;
-
- //read rest
- for (int i = 0; i < 15; i++) {
- if (!in.eof()) { in >> junk; }
- else { break; }
- }
- }
-
- m->gobble(in);
- }
- in.close();
- out.close();
-
- 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;
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "readAlign");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-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