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|
/*
* 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"
#include "counttable.h"
#include "fastqread.h"
#include "inputdata.h"
#include "contigsreport.hpp"
#include "alignreport.hpp"
//**********************************************************************************************************************
vector<string> RemoveSeqsCommand::setParameters(){
try {
CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "FNGLT", "none","fastq",false,false,true); parameters.push_back(pfastq);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none","contigsreport",false,false); parameters.push_back(pcontigsreport);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["fastq"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["contigsreport"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["count"] = tempOutNames;
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, count, list, taxonomy, quality, fastq, contigsreport 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, count, list, taxonomy, qfile, alignreport, contigsreport, fastq and dups. You must provide accnos and at least one of the file parameters.\n";
helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=illumina1.8+.\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";
;
return helpString;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string RemoveSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
else if (type == "fastq") { pattern = "[filename],pick,[extension]"; }
else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
else if (type == "name") { pattern = "[filename],pick,[extension]"; }
else if (type == "group") { pattern = "[filename],pick,[extension]"; }
else if (type == "count") { pattern = "[filename],pick,[extension]"; }
else if (type == "list") { pattern = "[filename],[distance],pick,[extension]"; }
else if (type == "qfile") { pattern = "[filename],pick,[extension]"; }
else if (type == "alignreport") { pattern = "[filename],pick.[extension]"; }
else if (type == "contigsreport") { pattern = "[filename],pick.[extension]"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(string accnos, pair<string,string> dupsFile, string dupsFileType) {
try {
names = util.readAccnos(accnos);
dups = true; abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["count"] = tempOutNames;
if (dupsFile.first != "") {
if (dupsFileType == "count") { readCount(dupsFile.first, dupsFile.second); }
else { readName(dupsFile.first, dupsFile.second); }
}
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand - mothurRun");
exit(1);
}
}
//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(unordered_set<string> n, pair<string,string> dupsFile, string dupsFileType) {
try {
names = n;
dups = true; abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["count"] = tempOutNames;
if (dupsFile.first != "") {
if (dupsFileType == "count") { readCount(dupsFile.first, dupsFile.second); }
else { readName(dupsFile.first, dupsFile.second); }
}
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand - mothurRun");
exit(1);
}
}
//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
accnosfile = validParameter.validFile(parameters, "accnos");
if (accnosfile == "not open") { abort = true; }
else if (accnosfile == "not found") {
accnosfile = current->getAccnosFile();
if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter.\n"); }
else {
m->mothurOut("[ERROR]: You have no valid accnos file and accnos is required.\n"); abort = true;
}
}else { current->setAccnosFile(accnosfile); }
fastafiles = validParameter.validFiles(parameters, "fasta");
if (fastafiles.size() != 0) {
if (fastafiles[0] == "not open") { abort = true; }
else { current->setFastaFile(fastafiles[0]); }
}
namefiles = validParameter.validFiles(parameters, "name");
if (namefiles.size() != 0) {
if (namefiles[0] == "not open") { abort = true; }
else { current->setNameFile(namefiles[0]); }
}
groupfiles = validParameter.validFiles(parameters, "group");
if (groupfiles.size() != 0) {
if (groupfiles[0] == "not open") { abort = true; }
else { current->setGroupFile(groupfiles[0]); }
}
alignfiles = validParameter.validFiles(parameters, "alignreport");
if (alignfiles.size() != 0) {
if (alignfiles[0] == "not open") { abort = true; }
}
contigsreportfiles = validParameter.validFiles(parameters, "contigsreport");
if (contigsreportfiles.size() != 0) {
if (contigsreportfiles[0] == "not open") { abort = true; }
else { current->setContigsReportFile(contigsreportfiles[0]); }
}
listfiles = validParameter.validFiles(parameters, "list");
if (listfiles.size() != 0) {
if (listfiles[0] == "not open") { abort = true; }
else { current->setListFile(listfiles[0]); }
}
taxfiles = validParameter.validFiles(parameters, "taxonomy");
if (taxfiles.size() != 0) {
if (taxfiles[0] == "not open") { abort = true; }
else { current->setTaxonomyFile(taxfiles[0]); }
}
countfiles = validParameter.validFiles(parameters, "count");
if (countfiles.size() != 0) {
if (countfiles[0] == "not open") { abort = true; }
else { current->setCountFile(countfiles[0]); }
}
fastqfiles = validParameter.validFiles(parameters, "fastq");
if (fastqfiles.size() != 0) {
if (fastqfiles[0] == "not open") { abort = true; }
}
qualityfiles = validParameter.validFiles(parameters, "qfile");
if (qualityfiles.size() != 0) {
if (qualityfiles[0] == "not open") { abort = true; }
else { current->setQualFile(qualityfiles[0]); }
}
if ((qualityfiles.size() == 0) && (fastqfiles.size() == 0) && (countfiles.size() == 0) && (fastafiles.size() == 0) && (namefiles.size() == 0) && (listfiles.size() == 0) && (groupfiles.size() == 0) && (alignfiles.size() == 0) && (taxfiles.size() == 0) && (contigsreportfiles.size() == 0)) { m->mothurOut("You must provide a file.\n"); abort = true; }
string usedDups = "true";
string temp = validParameter.valid(parameters, "dups");
if (temp == "not found") {
if (namefiles.size() != 0) { temp = "true"; }
else { temp = "false"; usedDups = ""; }
}
dups = util.isTrue(temp);
format = validParameter.valid(parameters, "format"); if (format == "not found"){ format = "illumina1.8+"; }
if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa")) {
m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, aborting.\n" ); abort=true;
}
}
if (!abort) { names = util.readAccnos(accnosfile); }
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveSeqsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (m->getControl_pressed()) { return 0; }
//read through the correct file and output lines you want to keep
if (namefiles.size() != 0) { for (int i = 0; i < namefiles.size(); i++) { readName(namefiles[i]); } }
if (fastafiles.size() != 0) { for (int i = 0; i < fastafiles.size(); i++) { readFasta(fastafiles[i]); } }
if (qualityfiles.size() != 0) { for (int i = 0; i < qualityfiles.size(); i++) { readQual(qualityfiles[i]); } }
if (groupfiles.size() != 0) { for (int i = 0; i < groupfiles.size(); i++) { readGroup(groupfiles[i]); } }
if (taxfiles.size() != 0) { for (int i = 0; i < taxfiles.size(); i++) { readTax(taxfiles[i]); } }
if (listfiles.size() != 0) { for (int i = 0; i < listfiles.size(); i++) { readList(listfiles[i]); } }
if (alignfiles.size() != 0) { for (int i = 0; i < alignfiles.size(); i++) { readAlign(alignfiles[i]); } }
if (countfiles.size() != 0) { for (int i = 0; i < countfiles.size(); i++) { readCount(countfiles[i]); } }
if (fastqfiles.size() != 0) { for (int i = 0; i < fastqfiles.size(); i++) { readFastq(fastqfiles[i]); } }
if (contigsreportfiles.size() != 0) { for (int i = 0; i < contigsreportfiles.size(); i++) { readContigs(contigsreportfiles[i]); } }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File Names:\n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]+"\n"); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setNameFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setListFile(currentName); }
}
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setTaxonomyFile(currentName); }
}
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setQualFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readFasta(string fastafile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(fastafile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastafile));
variables["[extension]"] = util.getExtension(fastafile);
string outputFileName = getOutputFileName("fasta", variables);
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(fastafile, in);
string name; bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
while(!in.eof()){
if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); return; }
Sequence currSeq(in);
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(currSeq.getName());
if (it != uniqueMap.end()) { currSeq.setName(it->second); }
}
name = currSeq.getName();
if (name != "") {
//if this name is in the accnos file
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
uniqueNames.insert(name);
wroteSomething = true;
currSeq.printSequence(out);
}else {
m->mothurOut("[WARNING]: " + name + " is in your fasta file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
}
gobble(in);
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + fastafile + " contains only sequences from the .accnos file.\n"); }
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + fastafile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readFasta");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readGZFastq(string fastqfile){
try {
#ifdef USE_BOOST
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(fastqfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastqfile));
variables["[extension]"] = ".fastq" + util.getExtension(fastqfile);
string outputFileName = getOutputFileName("fastq", variables);
ifstream in; boost::iostreams::filtering_istream inBoost;
util.openInputFileBinary(fastqfile, in, inBoost);
ofstream file; ostream* out; boost::iostreams::filtering_streambuf<boost::iostreams::output> outBoost;
util.openOutputFileBinary(outputFileName, file, out, outBoost);
bool wroteSomething = false; int removedCount = 0; set<string> uniqueNames;
while(!inBoost.eof()){
if (m->getControl_pressed()) { break; }
//read sequence name
bool ignore;
FastqRead fread(inBoost, ignore, format); gobble(inBoost);
if (!ignore) {
string name = fread.getName();
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
wroteSomething = true;
fread.printFastq(*out);
uniqueNames.insert(name);
}else {
m->mothurOut("[WARNING]: " + name + " is in your fastq file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
}
gobble(inBoost);
}
in.close(); inBoost.pop();
boost::iostreams::close(outBoost);
file.close(); delete out;
if (m->getControl_pressed()) { util.mothurRemove(outputFileName); return; }
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + fastqfile + " contains only sequences from the .accnos file.\n"); }
outputNames.push_back(outputFileName); outputTypes["fastq"].push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + fastqfile + ".\n");
#else
m->mothurOut("[ERROR]: mothur requires the boost libraries to read and write compressed files. Please decompress your files and rerun.\n");
#endif
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readFastq");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readFastq(string fastqfile){
try {
bool gz = util.isGZ(fastqfile)[1];
if (gz) { readGZFastq(fastqfile); return; }
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(fastqfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastqfile));
variables["[extension]"] = util.getExtension(fastqfile);
string outputFileName = getOutputFileName("fastq", variables);
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(fastqfile, in);
bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
while(!in.eof()){
if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); return; }
//read sequence name
bool ignore; FastqRead fread(in, ignore, format); gobble(in);
if (!ignore) {
string name = fread.getName();
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
wroteSomething = true;
fread.printFastq(out);
uniqueNames.insert(name);
}else {
m->mothurOut("[WARNING]: " + name + " is in your fastq file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
}
gobble(in);
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + fastqfile + " contains only sequences from the .accnos file.\n"); }
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + fastqfile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readFastq");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readQual(string qualfile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile));
variables["[extension]"] = util.getExtension(qualfile);
string outputFileName = getOutputFileName("qfile", variables);
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(qualfile, in);
string name; bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
while(!in.eof()){
QualityScores qual(in); gobble(in);
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(qual.getName());
if (it != uniqueMap.end()) { qual.setName(it->second); }
}
string name = qual.getName();
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
uniqueNames.insert(name);
wroteSomething = true;
qual.printQScores(out);
}else {
m->mothurOut("[WARNING]: " + name + " is in your qfile more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
gobble(in);
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + qualfile + " contains only sequences from the .accnos file.\n"); }
outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + qualfile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readQual");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readCount(string countfile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(countfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
variables["[extension]"] = util.getExtension(countfile);
string outputFileName = getOutputFileName("count", variables);
readCount(countfile, outputFileName);
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readCount");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readCount(string countfile, string outputFileName){
try {
CountTable ct; ct.readTable(countfile, true, false); int originalCount = ct.getNumSeqs();
for (auto it = names.begin(); it != names.end(); it++) {
ct.zeroOutSeq(*it);
if (m->getControl_pressed()) { return; }
}
ct.printTable(outputFileName);
int removedCount = originalCount - ct.getNumSeqs();
outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + countfile + ".\n");
if (ct.getNumSeqs() == 0) { m->mothurOut("[WARNING]: " + countfile + " contains only sequences from the .accnos file.\n"); }
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readCount");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readList(string listfile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(listfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(listfile));
variables["[extension]"] = util.getExtension(listfile);
InputData input(listfile, "list", nullVector);
ListVector* list = input.getListVector();
bool wroteSomething = false; int removedCount = 0;
while(list != nullptr) {
removedCount = 0;
set<string> uniqueNames;
//make a new list vector
ListVector newList;
newList.setLabel(list->getLabel());
variables["[distance]"] = list->getLabel();
string outputFileName = getOutputFileName("list", variables);
ofstream out;
util.openOutputFile(outputFileName, out);
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
vector<string> binLabels = list->getLabels();
vector<string> newBinLabels;
if (m->getControl_pressed()) { out.close(); return; }
//for each bin
for (int i = 0; i < list->getNumBins(); i++) {
if (m->getControl_pressed()) { out.close(); util.mothurRemove(outputFileName); return; }
//parse out names that are in accnos file
string bin = list->get(i);
vector<string> bnames;
util.splitAtComma(bin, bnames);
string newNames = "";
for (int j = 0; j < bnames.size(); j++) {
string name = bnames[j];
//if that name is in the .accnos file, add it
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
uniqueNames.insert(name);
newNames += name + ",";
}else {
m->mothurOut("[WARNING]: " + name + " is in your list file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}
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);
newBinLabels.push_back(binLabels[i]);
}
}
//print new listvector
if (newList.getNumBins() != 0) {
wroteSomething = true;
newList.setLabels(newBinLabels);
newList.print(out, false);
}
out.close();
delete list;
list = input.getListVector();
}
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + listfile + " contains only sequences from the .accnos file.\n"); }
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + listfile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readList");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readName(string namefile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(namefile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(namefile));
variables["[extension]"] = util.getExtension(namefile);
string outputFileName = getOutputFileName("name", variables);
readName(namefile, outputFileName);
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readList");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readName(string namefile, string outputFileName){
try {
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(namefile, in);
string name, firstCol, secondCol; bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
while(!in.eof()){
if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); return; }
in >> firstCol; gobble(in);
in >> secondCol; gobble(in);
vector<string> parsedNames;
util.splitAtComma(secondCol, parsedNames);
vector<string> validSecond; validSecond.clear(); vector<string> parsedNames2;
bool parsedError = false;
for (int i = 0; i < parsedNames.size(); i++) {
if (names.count(parsedNames[i]) == 0) {
if (uniqueNames.count(parsedNames[i]) == 0) { //this name hasn't been seen yet
uniqueNames.insert(parsedNames[i]);
validSecond.push_back(parsedNames[i]);
parsedNames2.push_back(parsedNames[i]);
}else {
m->mothurOut("[WARNING]: " + parsedNames[i] + " is in your name file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
parsedError = true;
}
}
}
if (parsedError) { parsedNames = parsedNames2; }
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 (validSecond.size() != 0) {
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';
//we are changing the unique name in the fasta file
uniqueMap[firstCol] = validSecond[0];
//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;
}
}
}
}
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + namefile + " contains only sequences from the .accnos file.\n"); }
outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + namefile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readName");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readGroup(string groupfile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(groupfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(groupfile));
variables["[extension]"] = util.getExtension(groupfile);
string outputFileName = getOutputFileName("group", variables);
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(groupfile, in);
string name, group; bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
while(!in.eof()){
if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); return; }
in >> name; gobble(in); //read from first column
in >> group; //read from second column
//if this name is in the accnos file
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
uniqueNames.insert(name);
wroteSomething = true;
out << name << '\t' << group << endl;
}else {
m->mothurOut("[WARNING]: " + name + " is in your group file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
gobble(in);
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + groupfile + " contains only sequences from the .accnos file.\n"); }
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + groupfile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readGroup");
exit(1);
}
}
//**********************************************************************************************************************
void RemoveSeqsCommand::readTax(string taxfile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(taxfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(taxfile));
variables["[extension]"] = util.getExtension(taxfile);
string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(taxfile, in);
string name, tax; bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
while(!in.eof()){
if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); return; }
in >> name; gobble(in);
tax = util.getline(in); gobble(in);
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { name = it->second; }
}
//if this name is in the accnos file
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
uniqueNames.insert(name);
wroteSomething = true;
out << name << '\t' << tax << endl;
}else {
m->mothurOut("[WARNING]: " + name + " is in your taxonomy file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + taxfile + " contains only sequences from the .accnos file.\n"); }
outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + taxfile + ".\n");
return;
}
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
void RemoveSeqsCommand::readAlign(string alignfile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(alignfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(alignfile));
variables["[extension]"] = util.getExtension(alignfile);
string outputFileName = getOutputFileName("alignreport", variables);
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(alignfile, in);
bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
AlignReport report; report.readHeaders(in); gobble(in); report.printHeaders(out);
while(!in.eof()){
if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); return; }
report.read(in); gobble(in);
string name = report.getQueryName();
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { name = it->second; }
}
//if this name is in the accnos file
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
uniqueNames.insert(name);
wroteSomething = true;
report.print(out);
}else {
m->mothurOut("[WARNING]: " + name + " is in your alignreport file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + alignfile + " contains only sequences from the .accnos file.\n"); ofstream out1; util.openOutputFile(outputFileName, out1); out1.close(); }
outputTypes["alignreport"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + alignfile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readAlign");
exit(1);
}
}
//**********************************************************************************************************************
//contigsreport file has a column header line then all other lines contain 8 columns. we just want the first column since that contains the name
void RemoveSeqsCommand::readContigs(string contigsreportfile){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(contigsreportfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(contigsreportfile));
variables["[extension]"] = util.getExtension(contigsreportfile);
string outputFileName = getOutputFileName("contigsreport", variables);
ofstream out; util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(contigsreportfile, in);
bool wroteSomething = false; int removedCount = 0;
set<string> uniqueNames;
ContigsReport report; report.readHeaders(in); gobble(in); report.printHeaders(out);
while(!in.eof()){
if (m->getControl_pressed()) { break; }
report.read(in); gobble(in);
string name = report.getName();
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { name = it->second; }
}
if (names.count(name) == 0) {
if (uniqueNames.count(name) == 0) { //this name hasn't been seen yet
uniqueNames.insert(name);
wroteSomething = true;
report.print(out);
}else {
m->mothurOut("[WARNING]: " + name + " is in your contigsreport file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
}
in.close(); out.close();
if (wroteSomething == false) { m->mothurOut("[WARNING]: " + contigsreportfile + " only contains sequences from the .accnos file, everything removed.\n"); ofstream out1; util.openOutputFile(outputFileName, out1); out1.close(); } //reopening file clears header line
outputNames.push_back(outputFileName); outputTypes["contigsreport"].push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from " + contigsreportfile + ".\n");
return;
}
catch(exception& e) {
m->errorOut(e, "RemoveSeqsCommand", "readContigs");
exit(1);
}
}
//**********************************************************************************************************************
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