#include "getlineagecommand.h"
#include "sequence.hpp"
#include "listvector.hpp"
-
+#include "counttable.h"
+#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> GetLineageCommand::getValidParameters(){
+vector<string> GetLineageCommand::setParameters(){
try {
- string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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 pshared("shared", "InputTypes", "", "", "none", "FNGLT", "none","shared",false,false, true); parameters.push_back(pshared);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "tax", "FNGLT", "none","taxonomy",false,false, true); parameters.push_back(ptaxonomy);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "tax", "FNGLT", "none","constaxonomy",false,false, true); parameters.push_back(pconstaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter ptaxon("taxon", "String", "", "", "", "", "","",false,true, true); parameters.push_back(ptaxon);
+ 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, "GetLineageCommand", "getValidParameters");
+ m->errorOut(e, "GetLineageCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-GetLineageCommand::GetLineageCommand(){
+string GetLineageCommand::getHelpString(){
try {
- 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;
+ string helpString = "";
+ helpString += "The get.lineage command reads a taxonomy or constaxonomy file and any of the following file types: fasta, name, group, count, list, shared or alignreport file. The constaxonomy can only be used with a shared or list file.\n";
+ helpString += "It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n";
+ helpString += "The get.lineage command parameters are taxon, fasta, name, group, count, list, shared, taxonomy, alignreport, label and dups. You must provide taxonomy or constaxonomy unless you have a valid current taxonomy file.\n";
+ helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
+ helpString += "The taxon parameter allows you to select the taxons you would like to get and is required.\n";
+ helpString += "You may enter your taxons with confidence scores, doing so will get only those sequences that belong to the taxonomy and whose cofidence scores is above the scores you give.\n";
+ helpString += "If they belong to the taxonomy and have confidences below those you provide the sequence will not be selected.\n";
+ helpString += "The label parameter is used to analyze specific labels in your input. \n";
+ helpString += "The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
+ helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
+ helpString += "Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n";
+ helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\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, "GetLineageCommand", "GetLineageCommand");
+ m->errorOut(e, "GetLineageCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> GetLineageCommand::getRequiredParameters(){
- try {
- string Array[] = {"taxonomy","taxon"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetLineageCommand", "getRequiredParameters");
- exit(1);
- }
+string GetLineageCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "constaxonomy") { 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],pick,[extension]-[filename],[distance],pick,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[distance],pick,[extension]"; }
+ else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> GetLineageCommand::getRequiredFiles(){
+GetLineageCommand::GetLineageCommand(){
try {
- vector<string> myArray;
- return myArray;
+ 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["count"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "GetLineageCommand", "getRequiredFiles");
+ m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetLineageCommand::GetLineageCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
outputTypes["group"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["list"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
+ outputTypes["shared"] = 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 has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("constaxonomy");
+ //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["constaxonomy"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("shared");
+ //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["shared"] = 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 = ""; }
+ 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") { abort = 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; }
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 = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine(); abort = true; }
-
+ if (taxfile == "not open") { taxfile = ""; abort = true; }
+ else if (taxfile == "not found") { taxfile = ""; }
+ else { m->setTaxonomyFile(taxfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
+
+
+ constaxonomy = validParameter.validFile(parameters, "constaxonomy", true);
+ if (constaxonomy == "not open") { constaxonomy = ""; abort = true; }
+ else if (constaxonomy == "not found") { constaxonomy = ""; }
+
+ if ((constaxonomy == "") && (taxfile == "")) {
+ taxfile = m->getTaxonomyFile();
+ if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current taxonomy file and did not provide a constaxonomy file. The taxonomy or constaxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+
string usedDups = "true";
- string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; }
+ string temp = validParameter.validFile(parameters, "dups", false);
+ if (temp == "not found") {
+ if (namefile != "") { temp = "true"; }
+ else { temp = "false"; usedDups = ""; }
+ }
dups = m->isTrue(temp);
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
taxons = validParameter.validFile(parameters, "taxon", false);
if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; }
if (taxons[0] == '\'') { taxons = taxons.substr(1); }
if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
}
+ m->splitAtChar(taxons, listOfTaxons, '-');
-
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
-
- if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
-
+ if ((fastafile == "") && (constaxonomy == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy, constaxonomy, shared or listfile."); m->mothurOutEndLine(); abort = true; }
+
+ if ((constaxonomy != "") && ((fastafile != "") || (namefile != "") || (groupfile != "") || (alignfile != "") || (taxfile != "") || (countfile != ""))) {
+ m->mothurOut("[ERROR]: can only use constaxonomy file with a list or shared file, aborting.\n"); abort = true;
+ }
+
+ if ((constaxonomy != "") && (taxfile != "")) {
+ m->mothurOut("[ERROR]: Choose only one: taxonomy or constaxonomy, aborting.\n"); abort = true;
+ }
+
+ if ((sharedfile != "") && (taxfile != "")) {
+ m->mothurOut("[ERROR]: sharedfile can only be used with constaxonomy file, aborting.\n"); abort = true;
+ }
+
+ if ((sharedfile != "") || (listfile != "")) {
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
+ }
+
+ if (countfile == "") {
+ if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+ vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+ parser.getNameFile(files);
+ }
+ }
}
}
}
//**********************************************************************************************************************
-void GetLineageCommand::help(){
- try {
- m->mothurOut("The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n");
- m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n");
- m->mothurOut("The get.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy and taxon.\n");
- m->mothurOut("The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n");
- m->mothurOut("The taxon parameter allows you to select the taxons you would like to get.\n");
- m->mothurOut("The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
- m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
- m->mothurOut("Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n");
- m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "GetLineageCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int GetLineageCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (m->control_pressed) { return 0; }
+
+ if (countfile != "") {
+ if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
+ m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
+ }
+ }
//read through the correct file and output lines you want to keep
- if (taxfile != "") { readTax(); } //fills the set of names to get
- if (namefile != "") { readName(); }
- if (fastafile != "") { readFasta(); }
- if (groupfile != "") { readGroup(); }
- if (alignfile != "") { readAlign(); }
- if (listfile != "") { readList(); }
-
+ if (taxfile != "") {
+ readTax(); //fills the set of names to get
+ if (namefile != "") { readName(); }
+ if (fastafile != "") { readFasta(); }
+ if (countfile != "") { readCount(); }
+ if (groupfile != "") { readGroup(); }
+ if (alignfile != "") { readAlign(); }
+ if (listfile != "") { readList(); }
+
+ }else {
+ readConsTax();
+ if (listfile != "") { readConsList(); }
+ if (sharedfile != "") { readShared(); }
+ }
+
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); 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("shared");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+ }
+
+ itTypes = outputTypes.find("taxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
}
return 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
in.close();
out.close();
- if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
return 0;
}
}
//**********************************************************************************************************************
+int GetLineageCommand::readCount(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(countfile, in);
+
+ bool wroteSomething = false;
+
+ string headers = m->getline(in); m->gobble(in);
+ out << headers << endl;
+
+ string name, rest; int thisTotal;
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; m->gobble(in);
+ in >> thisTotal; m->gobble(in);
+ rest = m->getline(in); m->gobble(in);
+ if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
+
+ if (names.count(name) != 0) {
+ out << name << '\t' << thisTotal << '\t' << rest << endl;
+ wroteSomething = true;
+ }
+ }
+ in.close();
+ out.close();
+
+ //check for groups that have been eliminated
+ CountTable ct;
+ if (ct.testGroups(outputFileName)) {
+ ct.readTable(outputFileName, true);
+ ct.printTable(outputFileName);
+ }
+
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readCount");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
int GetLineageCommand::readList(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
//read in list vector
ListVector list(in);
//parse out names that are in accnos file
string binnames = list.get(i);
+ vector<string> bnames;
+ m->splitAtComma(binnames, bnames);
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());
-
+ 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) { newNames += name + ","; }
}
-
- //get last name
- if (names.count(binnames) != 0) { newNames += binnames + ","; }
+
//if there are names in this bin add to new list
if (newNames != "") {
in.close();
out.close();
- if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
return 0;
exit(1);
}
}
+//**********************************************************************************************************************
+int GetLineageCommand::readConsList(){
+ try {
+ getListVector();
+
+ if (m->control_pressed) { delete list; return 0;}
+
+ ListVector newList;
+ newList.setLabel(list->getLabel());
+ int selectedCount = 0;
+ bool wroteSomething = false;
+ string snumBins = toString(list->getNumBins());
+
+ for (int i = 0; i < list->getNumBins(); i++) {
+
+ if (m->control_pressed) { delete list; return 0;}
+
+ //create a label for this otu
+ string otuLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { otuLabel += "0"; }
+ }
+ otuLabel += sbinNumber;
+
+ if (names.count(otuLabel) != 0) {
+ selectedCount++;
+ newList.push_back(list->get(i));
+ }
+ }
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ variables["[distance]"] = list->getLabel();
+ string outputFileName = getOutputFileName("list", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ delete list;
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain OTUs from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
+
+ m->mothurOut("Selected " + toString(selectedCount) + " OTUs from your list file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readConsList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::getListVector(){
+ try {
+ InputData input(listfile, "list");
+ list = input.getListVector();
+ string lastLabel = list->getLabel();
+
+ if (label == "") { label = lastLabel; return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return 0; }
+
+ if(labels.count(list->getLabel()) == 1){
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector(lastLabel);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = list->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ delete list;
+ list = input.getListVector();
+ }
+
+
+ if (m->control_pressed) { return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ delete list;
+ list = input.getListVector(lastLabel);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getListVector");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetLineageCommand::readShared(){
+ try {
+
+ getShared();
+
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+
+ vector<string> newLabels;
+
+ //create new "filtered" lookup
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < lookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(lookup[i]->getLabel());
+ temp->setGroup(lookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ bool wroteSomething = false;
+ int numSelected = 0;
+ for (int i = 0; i < lookup[0]->getNumBins(); i++) {
+
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
+
+ //is this otu on the list
+ if (names.count(m->currentBinLabels[i]) != 0) {
+ numSelected++; wroteSomething = true;
+ newLabels.push_back(m->currentBinLabels[i]);
+ for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
+ newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
+ }
+ }
+ }
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ variables["[distance]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
+
+ m->currentBinLabels = newLabels;
+
+ newLookup[0]->printHeaders(out);
+
+ for (int i = 0; i < newLookup.size(); i++) {
+ out << newLookup[i]->getLabel() << '\t' << newLookup[i]->getGroup() << '\t';
+ newLookup[i]->print(out);
+ }
+ out.close();
+
+ for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; }
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain OTUs from " + taxons + "."); m->mothurOutEndLine(); }
+
+ m->mothurOut("Selected " + toString(numSelected) + " OTUs from your shared file."); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::getShared(){
+ try {
+ InputData input(sharedfile, "sharedfile");
+ lookup = input.getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ if (label == "") { label = lastLabel; return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return 0; }
+
+ if(labels.count(lookup[0]->getLabel()) == 1){
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors();
+ }
+
+
+ if (m->control_pressed) { return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getShared");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
int GetLineageCommand::readName(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> firstCol;
in >> secondCol;
if (dups) { hold = secondCol; }
vector<string> parsedNames;
- //parse second column saving each name
- while (secondCol.find_first_of(',') != -1) {
- name = secondCol.substr(0,secondCol.find_first_of(','));
- secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
- parsedNames.push_back(name);
- }
-
- //get name after last ,
- parsedNames.push_back(secondCol);
+ m->splitAtComma(secondCol, parsedNames);
vector<string> validSecond;
for (int i = 0; i < parsedNames.size(); i++) {
in.close();
out.close();
- if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
return 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
in.close();
out.close();
- if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
return 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
m->openInputFile(taxfile, in);
string name, tax;
- bool wroteSomething = false;
+ //bool wroteSomething = false;
+ vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
+ vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
+ vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
+
+ for (int i = 0; i < listOfTaxons.size(); i++) {
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ int hasConPos = listOfTaxons[i].find_first_of('(');
+ if (hasConPos != string::npos) {
+ taxonsHasConfidence[i] = true;
+ searchTaxons[i] = getTaxons(listOfTaxons[i]);
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ m->removeConfidences(noConfidenceTaxons[i]);
+ }
+ }
+
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ 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
- string newtax = tax;
+ string noQuotesTax = m->removeQuotes(tax);
+
+ for (int j = 0; j < listOfTaxons.size(); j++) {
+
+ string newtax = noQuotesTax;
- //if the users file contains confidence scores we want to ignore them when searching for the taxons
- int hasConfidences = tax.find_first_of('(');
- if (hasConfidences != string::npos) {
- newtax = removeConfidences(tax);
- }
-
- int pos = newtax.find(taxons);
+ //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
+ if (!taxonsHasConfidence[j]) {
+ int hasConfidences = noQuotesTax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ newtax = noQuotesTax;
+ m->removeConfidences(newtax);
+ }
+
+ int pos = newtax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
+ }
+ }else{//if listOfTaxons[i] has them and you don't them remove taxons
+ int hasConfidences = noQuotesTax.find_first_of('(');
+ if (hasConfidences == string::npos) {
+
+ int pos = newtax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
+ }
+ }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
+ //first remove confidences from both and see if the taxonomy exists
+
+ string noNewTax = noQuotesTax;
+ int hasConfidences = noQuotesTax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ noNewTax = noQuotesTax;
+ m->removeConfidences(noNewTax);
+ }
+
+ int pos = noNewTax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //if yes, then are the confidences okay
+
+ bool good = true;
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
+
+ //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
+ //we want to "line them up", so we will find the the index where the searchstring starts
+ int index = 0;
+ for (int i = 0; i < usersTaxon.size(); i++) {
+
+ if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
+ index = i;
+ int spot = 0;
+ bool goodspot = true;
+ //is this really the start, or are we dealing with a taxon of the same name?
+ while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
+ if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
+ else { spot++; }
+ }
+
+ if (goodspot) { break; }
+ }
+ }
+
+ for (int i = 0; i < searchTaxons[j].size(); i++) {
+
+ if ((i+index) < usersTaxon.size()) { //just in case, should never be false
+ if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
+ good = false;
+ break;
+ }
+ }else {
+ good = false;
+ break;
+ }
+ }
+
+ //passed the test so add you
+ if (good) {
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ break;
+ }
+ }
+ }
+ }
- if (pos != string::npos) { //this sequence contains the taxon the user wants
- names.insert(name);
- out << name << '\t' << tax << endl;
}
m->gobble(in);
exit(1);
}
}
-/**************************************************************************************************/
-string GetLineageCommand::removeConfidences(string tax) {
+//**********************************************************************************************************************
+int GetLineageCommand::readConsTax(){
try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomy); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomy));
+ variables["[extension]"] = m->getExtension(constaxonomy);
+ string outputFileName = getOutputFileName("constaxonomy", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ ifstream in;
+ m->openInputFile(constaxonomy, in);
+ string otuLabel, tax;
+ int numReps;
+
+ //read headers
+ string headers = m->getline(in);
+ out << headers << endl;
+
+ //bool wroteSomething = false;
+ vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
+ vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
+ vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
+
+ for (int i = 0; i < listOfTaxons.size(); i++) {
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ int hasConPos = listOfTaxons[i].find_first_of('(');
+ if (hasConPos != string::npos) {
+ taxonsHasConfidence[i] = true;
+ searchTaxons[i] = getTaxons(listOfTaxons[i]);
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ m->removeConfidences(noConfidenceTaxons[i]);
+ }
+ }
+
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> otuLabel; m->gobble(in);
+ in >> numReps; m->gobble(in);
+ in >> tax; m->gobble(in);
+
+ string noQuotesTax = m->removeQuotes(tax);
+
+ for (int j = 0; j < listOfTaxons.size(); j++) {
+
+ string newtax = noQuotesTax;
+
+ //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
+ if (!taxonsHasConfidence[j]) {
+ int hasConfidences = noQuotesTax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ newtax = noQuotesTax;
+ m->removeConfidences(newtax);
+ }
+
+ int pos = newtax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(otuLabel);
+ out << otuLabel << '\t' << numReps << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
+ }
+ }else{//if listOfTaxons[i] has them and you don't them remove taxons
+ int hasConfidences = noQuotesTax.find_first_of('(');
+ if (hasConfidences == string::npos) {
+
+ int pos = newtax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(otuLabel);
+ out << otuLabel << '\t' << numReps << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
+ }
+ }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
+ //first remove confidences from both and see if the taxonomy exists
+
+ string noNewTax = noQuotesTax;
+ int hasConfidences = noQuotesTax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ noNewTax = noQuotesTax;
+ m->removeConfidences(noNewTax);
+ }
+
+ int pos = noNewTax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //if yes, then are the confidences okay
+
+ bool good = true;
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
+
+ //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
+ //we want to "line them up", so we will find the the index where the searchstring starts
+ int index = 0;
+ for (int i = 0; i < usersTaxon.size(); i++) {
+
+ if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
+ index = i;
+ int spot = 0;
+ bool goodspot = true;
+ //is this really the start, or are we dealing with a taxon of the same name?
+ while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
+ if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
+ else { spot++; }
+ }
+
+ if (goodspot) { break; }
+ }
+ }
+
+ for (int i = 0; i < searchTaxons[j].size(); i++) {
+
+ if ((i+index) < usersTaxon.size()) { //just in case, should never be false
+ if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
+ good = false;
+ break;
+ }
+ }else {
+ good = false;
+ break;
+ }
+ }
+
+ //passed the test so add you
+ if (good) {
+ names.insert(otuLabel);
+ out << otuLabel << '\t' << numReps << '\t' << tax << endl;
+ break;
+ }
+ }
+ }
+ }
+
+ }
+ }
+ in.close();
+ out.close();
+
+ if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any OTUs from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readConsTax");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
+ try {
+
+ vector< map<string, float> > t;
string taxon = "";
int taxLength = tax.length();
+
for(int i=0;i<taxLength;i++){
if(tax[i] == ';'){
- taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
- taxon += ";";
+
+ int openParen = taxon.find_last_of('(');
+ int closeParen = taxon.find_last_of(')');
+
+ string newtaxon, confidence;
+ if ((openParen != string::npos) && (closeParen != string::npos)) {
+ string confidenceScore = taxon.substr(openParen+1, (closeParen-(openParen+1)));
+ if (m->isNumeric1(confidenceScore)) { //its a confidence
+ newtaxon = taxon.substr(0, openParen); //rip off confidence
+ confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
+ }else { //its part of the taxon
+ newtaxon = taxon;
+ confidence = "0";
+ }
+ }else{
+ newtaxon = taxon;
+ confidence = "0";
+ }
+ float con = 0;
+ convert(confidence, con);
+
+ map<string, float> temp;
+ temp[newtaxon] = con;
+
+ t.push_back(temp);
+ taxon = "";
}
else{
taxon += tax[i];
+
}
}
-
- return taxon;
+
+ return t;
}
catch(exception& e) {
- m->errorOut(e, "GetLineageCommand", "removeConfidences");
+ m->errorOut(e, "GetLineageCommand", "getTaxons");
exit(1);
}
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
+ variables["[extension]"] = m->getExtension(alignfile);
+ string outputFileName = getOutputFileName("alignreport", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
in.close();
out.close();
- if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
return 0;
projects / mothur.git / blobdiff