X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedcommand.cpp;h=8d5d89c3a96843b5fd1c8aafa112f25c3b216e1f;hp=1150e53735481aea3377ec81f78c0d2544f324e6;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=fdfbfe59134dd7dd3e49d90609d129128ba2d370 diff --git a/sharedcommand.cpp b/sharedcommand.cpp index 1150e53..8d5d89c 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"; } + 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 { @@ -188,7 +182,11 @@ SharedCommand::SharedCommand(string option) { countfile = validParameter.validFile(parameters, "count", true); if (countfile == "not open") { countfile = ""; abort = true; } else if (countfile == "not found") { countfile = ""; } - else { m->setCountTableFile(countfile); } + else { + m->setCountTableFile(countfile); + CountTable temp; + if (!temp.testGroups(countfile)) { m->mothurOut("[ERROR]: Your count file does not have group info, aborting."); m->mothurOutEndLine(); abort=true; } + } if ((biomfile == "") && (listfile == "")) { //is there are current file available for either of these? @@ -259,8 +257,9 @@ int SharedCommand::execute(){ if (outputDir == "") { outputDir += m->hasPath(filename); } - filename = outputDir + m->getRootName(m->getSimpleName(filename)); - filename = filename + getOutputFileNameTag("shared"); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(filename)); + filename = getOutputFileName("shared",variables); outputNames.push_back(filename); outputTypes["shared"].push_back(filename); if (listfile != "") { createSharedFromListGroup(filename); } @@ -767,7 +766,7 @@ int SharedCommand::createSharedFromListGroup(string filename) { m->setAllGroups(allGroups); }else{ countTable = new CountTable(); - countTable->readTable(countfile); + countTable->readTable(countfile, true); } if (m->control_pressed) { return 0; } @@ -791,12 +790,15 @@ 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"; @@ -813,7 +815,9 @@ int SharedCommand::createSharedFromListGroup(string filename) { 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"))); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -825,7 +829,7 @@ int SharedCommand::createSharedFromListGroup(string filename) { int error = ListGroupSameSeqs(namesSeqs, SharedList); 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->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 @@ -845,8 +849,10 @@ int SharedCommand::createSharedFromListGroup(string filename) { groups += (m->getGroups())[i] + "."; } }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; @@ -872,7 +878,9 @@ int SharedCommand::createSharedFromListGroup(string filename) { 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"))); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -890,7 +898,9 @@ int SharedCommand::createSharedFromListGroup(string filename) { 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"))); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -920,7 +930,9 @@ int SharedCommand::createSharedFromListGroup(string filename) { 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"))); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -966,7 +978,9 @@ int SharedCommand::createSharedFromListGroup(string filename) { 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"))); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -986,7 +1000,9 @@ int SharedCommand::createSharedFromListGroup(string filename) { if (m->control_pressed) { m->mothurRemove(filename); - for (int i=0; imothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); } + for (int i=0; imothurRemove(rabundFIleName); } return 0; } @@ -1015,7 +1031,10 @@ 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(); } @@ -1043,7 +1062,10 @@ 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{ @@ -1083,8 +1105,12 @@ int SharedCommand::ListGroupSameSeqs(vector& groupMapsSeqs, SharedListVe for (int j = 0; j < listNames.size(); j++) { int num = groupNamesSeqs.count(listNames[j]); - if (num == 0) { error = 1; m->mothurOut("[ERROR]: " + listNames[j] + " is in your listfile and not in your groupfile. Please correct."); m->mothurOutEndLine(); } - else { groupNamesSeqs.erase(listNames[j]); } + if (num == 0) { + error = 1; + if (groupfile != "") { + m->mothurOut("[ERROR]: " + listNames[j] + " is in your listfile and not in your groupfile. Please correct."); m->mothurOutEndLine(); } + else{ m->mothurOut("[ERROR]: " + listNames[j] + " is in your listfile and not in your count file. Please correct."); m->mothurOutEndLine(); } + }else { groupNamesSeqs.erase(listNames[j]); } } }