From d3e27ba055f6765044b885cded5302d9cece161a Mon Sep 17 00:00:00 2001 From: SarahsWork 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 > > 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 names, int& size) { for (set::iterator it = names.begin(); it != names.end(); it++) { - //if namesfile include the names if (namefile != "") { @@ -377,7 +376,7 @@ string ClassifyTreeCommand::getTaxonomy(set 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 GetLineageCommand::setParameters(){ @@ -20,8 +21,11 @@ vector 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 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 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 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 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 labels; labels.insert(label); + set processedLabels; + set 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::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 newLabels; + + //create new "filtered" lookup + vector 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 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 labels; labels.insert(label); + set processedLabels; + set 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::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 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 taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false); + vector< vector< map > > searchTaxons; searchTaxons.resize(listOfTaxons.size()); + vector 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 > 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 > 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 names; vector 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 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 > 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 RemoveLineageCommand::setParameters(){ @@ -20,8 +21,11 @@ vector 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 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 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 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 labels; labels.insert(label); + set processedLabels; + set 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::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 newLabels; + + //create new "filtered" lookup + vector 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 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 labels; labels.insert(label); + set processedLabels; + set 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::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 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 taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false); + vector< vector< map > > searchTaxons; searchTaxons.resize(listOfTaxons.size()); + vector 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 > 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 > 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 names; vector 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 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 > 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> 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> 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