X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedcommand.cpp;h=3be9bb16f6cab3275edf0bbaf5f4372d002ff7b1;hp=542f8d346447322aea63491e092b97632449bd62;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d diff --git a/sharedcommand.cpp b/sharedcommand.cpp index 542f8d3..3be9bb1 100644 --- a/sharedcommand.cpp +++ b/sharedcommand.cpp @@ -19,15 +19,15 @@ inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* r //********************************************************************************************************************** vector SharedCommand::setParameters(){ try { - CommandParameter pbiom("biom", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "none",false,false); parameters.push_back(pbiom); - CommandParameter plist("list", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "ListGroup",false,false); parameters.push_back(plist); - CommandParameter pcount("count", "InputTypes", "", "", "", "GroupCount", "",false,false); parameters.push_back(pcount); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "GroupCount", "ListGroup",false,false); parameters.push_back(pgroup); + CommandParameter pbiom("biom", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "none","shared",false,false); parameters.push_back(pbiom); + CommandParameter plist("list", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "ListGroup","shared",false,false,true); parameters.push_back(plist); + CommandParameter pcount("count", "InputTypes", "", "", "none", "GroupCount", "none","",false,false); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "GroupCount", "ListGroup","",false,false,true); parameters.push_back(pgroup); //CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pgroups("groups", "String", "", "", "", "", "","group",false,false); parameters.push_back(pgroups); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -56,28 +56,22 @@ string SharedCommand::getHelpString(){ } } //********************************************************************************************************************** -string SharedCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string SharedCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //is this a type this command creates - it = outputTypes.find(type); - if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } - else { - if (type == "shared") { outputFileName = "shared"; } - else if (type == "rabund") { outputFileName = "rabund"; } - else if (type == "group") { outputFileName = "groups"; } - else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } - } - return outputFileName; - } - catch(exception& e) { - m->errorOut(e, "SharedCommand", "getOutputFileNameTag"); - exit(1); - } + if (type == "shared") { pattern = "[filename],shared-[filename],[distance],shared"; } + else if (type == "rabund") { pattern = "[filename],[group],rabund"; } + else if (type == "group") { pattern = "[filename],[group],groups"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "SharedCommand", "getOutputPattern"); + exit(1); + } } - //********************************************************************************************************************** SharedCommand::SharedCommand(){ try { @@ -255,20 +249,9 @@ int SharedCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } - - //getting output filename - string filename = ""; - if (listfile != "") { filename = listfile; } - else { filename = biomfile; } - - if (outputDir == "") { outputDir += m->hasPath(filename); } - - filename = outputDir + m->getRootName(m->getSimpleName(filename)); - filename = filename + getOutputFileNameTag("shared"); - outputNames.push_back(filename); outputTypes["shared"].push_back(filename); - - if (listfile != "") { createSharedFromListGroup(filename); } - else { createSharedFromBiom(filename); } + + if (listfile != "") { createSharedFromListGroup(); } + else { createSharedFromBiom(); } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } } @@ -302,8 +285,17 @@ int SharedCommand::execute(){ } } //********************************************************************************************************************** -int SharedCommand::createSharedFromBiom(string filename) { +int SharedCommand::createSharedFromBiom() { try { + //getting output filename + string filename = biomfile; + if (outputDir == "") { outputDir += m->hasPath(filename); } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(filename)); + filename = getOutputFileName("shared",variables); + outputNames.push_back(filename); outputTypes["shared"].push_back(filename); + ofstream out; m->openOutputFile(filename, out); @@ -463,7 +455,7 @@ int SharedCommand::createSharedFromBiom(string filename) { if (it == fileLines.end()) { m->mothurOut("[ERROR]: you file does not have a data provided.\n"); } else { string thisLine = it->second; - m->currentBinLabels = otuNames; + m->currentSharedBinLabels = otuNames; //read data vector lookup = readData(matrixFormat, thisLine, matrixElementType, groupNames, otuNames.size()); @@ -616,7 +608,7 @@ int SharedCommand::eliminateZeroOTUS(vector& thislookup) { for (int h = 0; h < diff; h++) { binLabel += "0"; } } binLabel += sbinNumber; - if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } + if (i < m->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; } newBinLabels.push_back(binLabel); } @@ -625,7 +617,7 @@ int SharedCommand::eliminateZeroOTUS(vector& thislookup) { for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } thislookup = newLookup; - m->currentBinLabels = newBinLabels; + m->currentSharedBinLabels = newBinLabels; return 0; @@ -755,10 +747,8 @@ string SharedCommand::getTag(string& line) { } } //********************************************************************************************************************** -int SharedCommand::createSharedFromListGroup(string filename) { +int SharedCommand::createSharedFromListGroup() { try { - ofstream out; - m->openOutputFile(filename, out); GroupMap* groupMap = NULL; CountTable* countTable = NULL; @@ -771,7 +761,7 @@ int SharedCommand::createSharedFromListGroup(string filename) { m->setAllGroups(allGroups); }else{ countTable = new CountTable(); - countTable->readTable(countfile); + countTable->readTable(countfile, true, false); } if (m->control_pressed) { return 0; } @@ -785,6 +775,20 @@ int SharedCommand::createSharedFromListGroup(string filename) { m->setGroups(Groups); }else { pickedGroups = true; } + + ofstream out; + string filename = ""; + if (!pickedGroups) { + string filename = listfile; + if (outputDir == "") { outputDir += m->hasPath(filename); } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(filename)); + filename = getOutputFileName("shared",variables); + outputNames.push_back(filename); outputTypes["shared"].push_back(filename); + m->openOutputFile(filename, out); + } + //fill filehandles with neccessary ofstreams int i; ofstream* temp; @@ -795,12 +799,15 @@ int SharedCommand::createSharedFromListGroup(string filename) { //set fileroot fileroot = outputDir + m->getRootName(m->getSimpleName(listfile)); - + map variables; + variables["[filename]"] = fileroot; //clears file before we start to write to it below for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); - outputNames.push_back((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); - outputTypes["rabund"].push_back((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); + variables["[group]"] = Groups[i]; + string rabundFIleName = getOutputFileName("rabund",variables); + m->mothurRemove(rabundFIleName); + outputNames.push_back(rabundFIleName); + outputTypes["rabund"].push_back(rabundFIleName); } string errorOff = "no error"; @@ -816,8 +823,10 @@ int SharedCommand::createSharedFromListGroup(string filename) { if (m->control_pressed) { delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; } for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - out.close(); m->mothurRemove(filename); - for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); } + out.close(); if (!pickedGroups) { m->mothurRemove(filename); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -831,7 +840,7 @@ int SharedCommand::createSharedFromListGroup(string filename) { if ((!pickedGroups) && (SharedList->getNumSeqs() != numGroupNames)) { //if the user has not specified any groups and their files don't match exit with error m->mothurOut("Your group file contains " + toString(numGroupNames) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine(); m->control_pressed = true; - out.close(); m->mothurRemove(filename); //remove blank shared file you made + out.close(); if (!pickedGroups) { m->mothurRemove(filename); } //remove blank shared file you made //delete memory for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } @@ -845,12 +854,15 @@ int SharedCommand::createSharedFromListGroup(string filename) { if ((pickedGroups) && (m->groupMode == "group")) { //make new group file string groups = ""; if (m->getNumGroups() < 4) { - for (int i = 0; i < m->getNumGroups(); i++) { + for (int i = 0; i < m->getNumGroups()-1; i++) { groups += (m->getGroups())[i] + "."; } + groups+=(m->getGroups())[m->getNumGroups()-1]; }else { groups = "merge"; } - - string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + getOutputFileNameTag("group"); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[group]"] = groups; + string newGroupFile = getOutputFileName("group",variables); outputTypes["group"].push_back(newGroupFile); outputNames.push_back(newGroupFile); ofstream outGroups; @@ -875,8 +887,10 @@ int SharedCommand::createSharedFromListGroup(string filename) { if (m->control_pressed) { delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; } for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - out.close(); m->mothurRemove(filename); - for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); } + if (!pickedGroups) { out.close(); m->mothurRemove(filename); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -885,21 +899,42 @@ int SharedCommand::createSharedFromListGroup(string filename) { lookup = SharedList->getSharedRAbundVector(); m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - if (pickedGroups) { //check for otus with no seqs in them - eliminateZeroOTUS(lookup); - } if (m->control_pressed) { delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - out.close(); m->mothurRemove(filename); - for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); } + if (!pickedGroups) { out.close(); m->mothurRemove(filename); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } - if (!m->printedHeaders) { lookup[0]->printHeaders(out); } - printSharedData(lookup, out); //prints info to the .shared file + //if picked groups must split the shared file by label + if (pickedGroups) { + string filename = listfile; + if (outputDir == "") { outputDir += m->hasPath(filename); } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(filename)); + variables["[distance]"] = lookup[0]->getLabel(); + filename = getOutputFileName("shared",variables); + outputNames.push_back(filename); outputTypes["shared"].push_back(filename); + ofstream out2; + m->openOutputFile(filename, out2); + + vector savedLabels = m->currentSharedBinLabels; + eliminateZeroOTUS(lookup); + lookup[0]->printHeaders(out2); + printSharedData(lookup, out2); + out2.close(); + m->currentSharedBinLabels = savedLabels; //restore old labels + + }else { + if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); } + printSharedData(lookup, out); //prints info to the .shared file + } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } processedLabels.insert(SharedList->getLabel()); @@ -914,22 +949,43 @@ int SharedCommand::createSharedFromListGroup(string filename) { lookup = SharedList->getSharedRAbundVector(); m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - if (pickedGroups) { //check for otus with no seqs in them - eliminateZeroOTUS(lookup); - } - if (m->control_pressed) { delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - out.close(); m->mothurRemove(filename); - for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); } + if (!pickedGroups) { out.close(); m->mothurRemove(filename); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } - if (!m->printedHeaders) { lookup[0]->printHeaders(out); } - printSharedData(lookup, out); //prints info to the .shared file + //if picked groups must split the shared file by label + if (pickedGroups) { + string filename = listfile; + if (outputDir == "") { outputDir += m->hasPath(filename); } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(filename)); + variables["[distance]"] = lookup[0]->getLabel(); + filename = getOutputFileName("shared",variables); + outputNames.push_back(filename); outputTypes["shared"].push_back(filename); + ofstream out2; + m->openOutputFile(filename, out2); + + vector savedLabels = m->currentSharedBinLabels; + eliminateZeroOTUS(lookup); + lookup[0]->printHeaders(out2); + printSharedData(lookup, out2); + out2.close(); + m->currentSharedBinLabels = savedLabels; //restore old labels + + }else { + if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); } + printSharedData(lookup, out); //prints info to the .shared file + } + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } processedLabels.insert(SharedList->getLabel()); @@ -962,25 +1018,46 @@ int SharedCommand::createSharedFromListGroup(string filename) { lookup = SharedList->getSharedRAbundVector(); m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); - if (pickedGroups) { //check for otus with no seqs in them - eliminateZeroOTUS(lookup); - } if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; } for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - out.close(); m->mothurRemove(filename); - for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); } + if (!pickedGroups) { out.close(); m->mothurRemove(filename); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } - if (!m->printedHeaders) { lookup[0]->printHeaders(out); } - printSharedData(lookup, out); //prints info to the .shared file + //if picked groups must split the shared file by label + if (pickedGroups) { + string filename = listfile; + if (outputDir == "") { outputDir += m->hasPath(filename); } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(filename)); + variables["[distance]"] = lookup[0]->getLabel(); + filename = getOutputFileName("shared",variables); + outputNames.push_back(filename); outputTypes["shared"].push_back(filename); + ofstream out2; + m->openOutputFile(filename, out2); + + vector savedLabels = m->currentSharedBinLabels; + eliminateZeroOTUS(lookup); + lookup[0]->printHeaders(out2); + printSharedData(lookup, out2); + out2.close(); + m->currentSharedBinLabels = savedLabels; //restore old labels + + }else { + if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); } + printSharedData(lookup, out); //prints info to the .shared file + } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } delete SharedList; } - out.close(); + if (!pickedGroups) { out.close(); } for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; @@ -989,8 +1066,10 @@ int SharedCommand::createSharedFromListGroup(string filename) { if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; } if (m->control_pressed) { - m->mothurRemove(filename); - for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); } + if (!pickedGroups) { m->mothurRemove(filename); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -1019,7 +1098,10 @@ void SharedCommand::printSharedData(vector thislookup, ofst Groups.push_back(thislookup[i]->getGroup()); RAbundVector rav = thislookup[i]->getRAbundVector(); - m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + "." + getOutputFileNameTag("rabund"), *(filehandles[thislookup[i]->getGroup()])); + map variables; + variables["[filename]"] = fileroot; + variables["[group]"] = thislookup[i]->getGroup(); + m->openOutputFileAppend(getOutputFileName("rabund",variables), *(filehandles[thislookup[i]->getGroup()])); rav.print(*(filehandles[thislookup[i]->getGroup()])); (*(filehandles[thislookup[i]->getGroup()])).close(); } @@ -1047,7 +1129,10 @@ void SharedCommand::printSharedData(vector thislookup, ofst Groups.push_back((myIt->second)->getGroup()); RAbundVector rav = (myIt->second)->getRAbundVector(); - m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + "." + getOutputFileNameTag("rabund"), *(filehandles[(myIt->second)->getGroup()])); + map variables; + variables["[filename]"] = fileroot; + variables["[group]"] = (myIt->second)->getGroup(); + m->openOutputFileAppend(getOutputFileName("rabund",variables), *(filehandles[(myIt->second)->getGroup()])); rav.print(*(filehandles[(myIt->second)->getGroup()])); (*(filehandles[(myIt->second)->getGroup()])).close(); }else{