From d3e27ba055f6765044b885cded5302d9cece161a Mon Sep 17 00:00:00 2001
From: SarahsWork <sarahswork@imac.westcotts.net>
Date: Mon, 29 Apr 2013 11:58:15 -0400
Subject: [PATCH] added shared, constaxonomy and label parameter to get.lineage
and remove.lineage commands. Allows user to select / remove OTUs that
classified to a specific taxonomy or set of taxonomies.
---
classifytreecommand.cpp | 7 +-
countseqscommand.cpp | 13 +-
getlineagecommand.cpp | 575 +++++++++++++++++++++++++++++++++++---
getlineagecommand.h | 13 +-
removelineagecommand.cpp | 582 ++++++++++++++++++++++++++++++++++++---
removelineagecommand.h | 14 +-
sharedrabundvector.cpp | 7 +-
7 files changed, 1132 insertions(+), 79 deletions(-)
diff --git a/classifytreecommand.cpp b/classifytreecommand.cpp
index f1f1ffd..79a8245 100644
--- a/classifytreecommand.cpp
+++ b/classifytreecommand.cpp
@@ -303,7 +303,7 @@ int ClassifyTreeCommand::getClassifications(Tree*& T){
//create a map from tree node index to names of descendants, save time later
map<int, map<string, set<string> > > nodeToDescendants; //node# -> (groupName -> groupMembers)
for (int i = 0; i < T->getNumNodes(); i++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { return 0; }
nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants);
}
@@ -327,7 +327,7 @@ int ClassifyTreeCommand::getClassifications(Tree*& T){
tax = getTaxonomy(nodeToDescendants[i][group], size);
out << (i+1) << '\t' << size << '\t' << tax << endl;
}
-
+
T->tree[i].setLabel((i+1));
}
out.close();
@@ -356,7 +356,6 @@ string ClassifyTreeCommand::getTaxonomy(set<string> names, int& size) {
for (set<string>::iterator it = names.begin(); it != names.end(); it++) {
-
//if namesfile include the names
if (namefile != "") {
@@ -377,7 +376,7 @@ string ClassifyTreeCommand::getTaxonomy(set<string> names, int& size) {
}else{
//add seq to tree
int num = nameCount[(*it)]; // we know its there since we found it in nameMap
- for (int i = 0; i < num; i++) { phylo->addSeqToTree((*it)+toString(i), it2->second); }
+ for (int i = 0; i < num; i++) { phylo->addSeqToTree((*it)+toString(i), itTax->second); }
size += num;
}
}
diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 6afd1f4..411a814 100644
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -373,12 +373,13 @@ int CountSeqsCommand::createProcesses(GroupMap*& groupMap, string outputFileName
//sanity check
- if (numSeqs != groupMap->getNumSeqs()) {
- m->mothurOut("[ERROR]: processes reported processing " + toString(numSeqs) + " sequences, but group file indicates you have " + toString(groupMap->getNumSeqs()) + " sequences.");
- if (processors == 1) { m->mothurOut(" Could you have a file mismatch?\n"); }
- else { m->mothurOut(" Either you have a file mismatch or a process failed to complete the task assigned to it.\n"); m->control_pressed = true; }
- }
-
+ if (groupfile != "") {
+ if (numSeqs != groupMap->getNumSeqs()) {
+ m->mothurOut("[ERROR]: processes reported processing " + toString(numSeqs) + " sequences, but group file indicates you have " + toString(groupMap->getNumSeqs()) + " sequences.");
+ if (processors == 1) { m->mothurOut(" Could you have a file mismatch?\n"); }
+ else { m->mothurOut(" Either you have a file mismatch or a process failed to complete the task assigned to it.\n"); m->control_pressed = true; }
+ }
+ }
return numSeqs;
}
catch(exception& e) {
diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index b895cc4..25a68be 100644
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -11,6 +11,7 @@
#include "sequence.hpp"
#include "listvector.hpp"
#include "counttable.h"
+#include "inputdata.h"
//**********************************************************************************************************************
vector<string> GetLineageCommand::setParameters(){
@@ -20,8 +21,11 @@ vector<string> GetLineageCommand::setParameters(){
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,true, true); parameters.push_back(ptaxonomy);
+ 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);
@@ -40,13 +44,14 @@ vector<string> GetLineageCommand::setParameters(){
string GetLineageCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, count, list or alignreport file.\n";
+ 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, taxonomy, alignreport and dups. You must provide taxonomy unless you have a valid current taxonomy file.\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";
@@ -64,13 +69,15 @@ 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 == "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]"; }
- else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
+ 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;
@@ -93,6 +100,8 @@ GetLineageCommand::GetLineageCommand(){
outputTypes["alignreport"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["count"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
@@ -131,6 +140,8 @@ GetLineageCommand::GetLineageCommand(string option) {
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 = ""; }
@@ -195,6 +206,22 @@ GetLineageCommand::GetLineageCommand(string option) {
//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; }
+ }
}
@@ -225,12 +252,26 @@ GetLineageCommand::GetLineageCommand(string option) {
taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not open") { taxfile = ""; abort = true; }
- else if (taxfile == "not found") {
- 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 the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setTaxonomyFile(taxfile); }
-
+ 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") {
@@ -261,8 +302,25 @@ GetLineageCommand::GetLineageCommand(string option) {
}
m->splitAtChar(taxons, listOfTaxons, '-');
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy or listfile."); 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);
@@ -293,14 +351,21 @@ int GetLineageCommand::execute(){
}
//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 (countfile != "") { readCount(); }
- 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++) { m->mothurRemove(outputNames[i]); } return 0; }
@@ -331,6 +396,11 @@ int GetLineageCommand::execute(){
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()) {
@@ -492,18 +562,16 @@ int GetLineageCommand::readList(){
//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 != "") {
@@ -534,6 +602,292 @@ int GetLineageCommand::readList(){
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 {
@@ -824,6 +1178,161 @@ int GetLineageCommand::readTax(){
exit(1);
}
}
+//**********************************************************************************************************************
+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 {
diff --git a/getlineagecommand.h b/getlineagecommand.h
index 68f974f..4cee8b6 100644
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -11,6 +11,8 @@
*/
#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
class GetLineageCommand : public Command {
@@ -37,8 +39,10 @@ class GetLineageCommand : public Command {
private:
set<string> names;
vector<string> outputNames, listOfTaxons;
- string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons;
+ string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
bool abort, dups;
+ vector<SharedRAbundVector*> lookup;
+ ListVector* list;
int readFasta();
int readName();
@@ -46,7 +50,12 @@ class GetLineageCommand : public Command {
int readGroup();
int readAlign();
int readList();
- int readTax();
+ int readTax();
+ int readShared();
+ int readConsTax();
+ int readConsList();
+ int getShared();
+ int getListVector();
vector< map<string, float> > getTaxons(string);
};
diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 1496f8a..66bbc17 100644
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -11,6 +11,7 @@
#include "sequence.hpp"
#include "listvector.hpp"
#include "counttable.h"
+#include "inputdata.h"
//**********************************************************************************************************************
vector<string> RemoveLineageCommand::setParameters(){
@@ -20,8 +21,11 @@ vector<string> RemoveLineageCommand::setParameters(){
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,true,true); parameters.push_back(ptaxonomy);
+ 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);
@@ -40,13 +44,14 @@ vector<string> RemoveLineageCommand::setParameters(){
string RemoveLineageCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, count, list or alignreport file.\n";
- helpString += "It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n";
- helpString += "The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, count, alignreport and dups. You must provide taxonomy unless you have a valid current taxonomy file.\n";
+ helpString += "The remove.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 or OTUS from the taxonomy file that are not from the taxon you requested to be removed.\n";
+ helpString += "The remove.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 remove, and is required.\n";
helpString += "You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n";
helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n";
+ helpString += "The label parameter is used to analyze specific labels in your input. \n";
helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
helpString += "Example remove.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";
@@ -64,13 +69,15 @@ string RemoveLineageCommand::getOutputPattern(string type) {
try {
string pattern = "";
- if (type == "fasta") { 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],pick,[extension]"; }
- else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
+ 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;
@@ -94,6 +101,9 @@ RemoveLineageCommand::RemoveLineageCommand(){
outputTypes["alignreport"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["count"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
@@ -132,6 +142,9 @@ RemoveLineageCommand::RemoveLineageCommand(string option) {
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 = ""; }
@@ -196,6 +209,22 @@ RemoveLineageCommand::RemoveLineageCommand(string option) {
//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; }
+ }
}
@@ -226,11 +255,26 @@ RemoveLineageCommand::RemoveLineageCommand(string option) {
taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not open") { taxfile = ""; abort = true; }
- else if (taxfile == "not found") {
- 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 the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setTaxonomyFile(taxfile); }
+ 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; }
+ }
+
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
@@ -262,7 +306,25 @@ RemoveLineageCommand::RemoveLineageCommand(string option) {
}
m->splitAtChar(taxons, listOfTaxons, '-');
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy or listfile."); 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 ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
@@ -297,13 +359,20 @@ int RemoveLineageCommand::execute(){
}
//read through the correct file and output lines you want to keep
- if (taxfile != "") { readTax(); } //fills the set of names to remove
- if (namefile != "") { readName(); }
- if (fastafile != "") { readFasta(); }
- if (groupfile != "") { readGroup(); }
- if (alignfile != "") { readAlign(); }
- if (listfile != "") { readList(); }
- if (countfile != "") { readCount(); }
+ 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) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
@@ -435,18 +504,15 @@ int RemoveLineageCommand::readList(){
//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 != "") {
@@ -613,6 +679,292 @@ int RemoveLineageCommand::readCount(){
exit(1);
}
}
+//**********************************************************************************************************************
+int RemoveLineageCommand::readConsList(){
+ try {
+ getListVector();
+
+ if (m->control_pressed) { delete list; return 0;}
+
+ ListVector newList;
+ newList.setLabel(list->getLabel());
+ int removedCount = 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) {
+ newList.push_back(list->get(i));
+ }else { removedCount++; }
+ }
+
+ 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 only contains OTUs from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
+
+ m->mothurOut("Removed " + toString(removedCount) + " OTUs from your list file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readConsList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveLineageCommand::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, "RemoveLineageCommand", "getListVector");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int RemoveLineageCommand::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 numRemoved = 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) {
+ 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());
+ }
+ }else { numRemoved++; }
+ }
+
+ 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 only contains OTUs from " + taxons + "."); m->mothurOutEndLine(); }
+
+ m->mothurOut("Removed " + toString(numRemoved) + " OTUs from your shared file."); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveLineageCommand::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, "RemoveLineageCommand", "getShared");
+ exit(1);
+ }
+}
+
+
//**********************************************************************************************************************
int RemoveLineageCommand::readGroup(){
try {
@@ -821,6 +1173,174 @@ int RemoveLineageCommand::readTax(){
exit(1);
}
}
+//**********************************************************************************************************************
+int RemoveLineageCommand::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;
+ bool wroteSomething = false;
+
+ //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);
+
+ bool remove = false;
+
+ 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) {
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
+ }else{ //this sequence contains the taxon the user wants to remove
+ names.insert(otuLabel);
+ remove=true; break;
+ }
+
+ }else{//if taxons 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) {
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
+ }else{ //this sequence contains the taxon the user wants to remove
+ names.insert(otuLabel);
+ remove=true; 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
+
+ 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
+ remove = true;
+ break;
+ }
+ }else {
+ remove = true;
+ break;
+ }
+ }
+
+ //passed the test so remove you
+ if (remove) {
+ names.insert(otuLabel);
+ remove=true; break;
+ }else {
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
+ }
+ }else {
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
+ }
+ }
+ }
+
+ }
+
+ if (!remove) { wroteSomething = true; out << otuLabel << '\t' << numReps << '\t' << tax << endl; }
+
+ }
+ in.close();
+ out.close();
+
+ if (names.size() == 0) { m->mothurOut("Your constaxonomy file contains OTUs only from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "readConsTax");
+ exit(1);
+ }
+}
/**************************************************************************************************/
vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
try {
diff --git a/removelineagecommand.h b/removelineagecommand.h
index f644972..8bfa5f1 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -11,6 +11,9 @@
*/
#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
+
class RemoveLineageCommand : public Command {
@@ -35,8 +38,10 @@ class RemoveLineageCommand : public Command {
private:
set<string> names;
vector<string> outputNames, listOfTaxons;
- string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons;
+ string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
bool abort, dups;
+ vector<SharedRAbundVector*> lookup;
+ ListVector* list;
int readFasta();
int readName();
@@ -44,7 +49,12 @@ class RemoveLineageCommand : public Command {
int readCount();
int readAlign();
int readList();
- int readTax();
+ int readTax();
+ int readShared();
+ int readConsTax();
+ int readConsList();
+ int getShared();
+ int getListVector();
vector< map<string, float> > getTaxons(string);
};
diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 7bc333b..9b2bb67 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -72,7 +72,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
//are we at the beginning of the file??
if (m->saveNextLabel == "") {
f >> label;
-
+
//is this a shared file that has headers
if (label == "label") {
//gets "group"
@@ -120,6 +120,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
//read in first row since you know there is at least 1 group.
f >> groupN >> num;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
}
//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
@@ -138,6 +140,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
//fill vector. data = first sharedrabund in file
for(int i=0;i<num;i++){
f >> inputData;
+ if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
lookup[0]->push_back(inputData, groupN); //abundance, bin, group
push_back(inputData, groupN);
@@ -152,6 +155,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
//read the rest of the groups info in
while ((nextLabel == holdLabel) && (f.eof() != true)) {
f >> groupN >> num;
+ if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
count++;
allGroups.push_back(groupN);
@@ -165,6 +169,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
//fill vector.
for(int i=0;i<num;i++){
f >> inputData;
+ if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
lookup[count]->push_back(inputData, groupN); //abundance, bin, group
}
--
2.39.5