X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=33a0e6dd9a3128541ab57777125251a97effdefc;hb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;hp=1417b5a34a6e4ca8a133cc6f2c8ae390ffb81271;hpb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index 1417b5a..33a0e6d 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -9,6 +9,57 @@ #include "unifracweightedcommand.h" +//********************************************************************************************************************** +vector UnifracWeightedCommand::getValidParameters(){ + try { + string Array[] = {"groups","iters","distance","random","processors","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +UnifracWeightedCommand::UnifracWeightedCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["weighted"] = tempOutNames; + outputTypes["wsummary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector UnifracWeightedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector UnifracWeightedCommand::getRequiredFiles(){ + try { + string Array[] = {"tree","group"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "getRequiredFiles"); + exit(1); + } +} /***********************************************************/ UnifracWeightedCommand::UnifracWeightedCommand(string option) { try { @@ -34,6 +85,12 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["weighted"] = tempOutNames; + outputTypes["wsummary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; + if (globaldata->gTree.size() == 0) {//no trees were read m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; } @@ -72,7 +129,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { tmap = globaldata->gTreemap; sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".wsummary"; m->openOutputFile(sumFile, outSum); - outputNames.push_back(sumFile); + outputNames.push_back(sumFile); outputTypes["wsummary"].push_back(sumFile); util = new SharedUtil(); string s; //to make work with setgroups @@ -96,11 +153,12 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { void UnifracWeightedCommand::help(){ try { m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n"); - m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random. No parameters are required.\n"); + m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance, processors and random. No parameters are required.\n"); m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n"); m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n"); m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n"); m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n"); + m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n"); m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n"); m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n"); @@ -137,6 +195,7 @@ int UnifracWeightedCommand::execute() { if (random) { output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString); outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted"); + outputTypes["weighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted"); } userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore @@ -153,12 +212,11 @@ int UnifracWeightedCommand::execute() { } if (random) { - vector sums = weighted->getBranchLengthSums(T[i]); //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3; vector< vector > namesOfGroupCombos; for (int a=0; a groups; groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]); namesOfGroupCombos.push_back(groups); } @@ -187,12 +245,12 @@ int UnifracWeightedCommand::execute() { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ - driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores); + driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores); }else{ - createProcesses(T[i], namesOfGroupCombos, sums, rScores); + createProcesses(T[i], namesOfGroupCombos, rScores); } #else - driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores); + driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores); #endif if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } @@ -264,7 +322,7 @@ int UnifracWeightedCommand::execute() { } /**************************************************************************************************/ -int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > namesOfGroupCombos, vector& sums, vector< vector >& scores) { +int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > namesOfGroupCombos, vector< vector >& scores) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 1; @@ -281,7 +339,7 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > na processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later process++; }else if (pid == 0){ - driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums, scores); + driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, scores); //pass numSeqs to parent ofstream out; @@ -294,7 +352,7 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > na }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } } - driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums, scores); + driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores); //force parent to wait until all the processes are done for (int i=0;i<(processors-1);i++) { @@ -325,7 +383,7 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > na } /**************************************************************************************************/ -int UnifracWeightedCommand::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num, vector& sums, vector< vector >& scores) { +int UnifracWeightedCommand::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num, vector< vector >& scores) { try { Tree* randT = new Tree(); @@ -346,7 +404,7 @@ int UnifracWeightedCommand::driver(Tree* t, vector< vector > namesOfGrou if (m->control_pressed) { delete randT; return 0; } //get wscore of random tree - EstOutput randomData = weighted->getValues(randT, groupA, groupB, sums); + EstOutput randomData = weighted->getValues(randT, groupA, groupB); if (m->control_pressed) { delete randT; return 0; } @@ -437,6 +495,7 @@ void UnifracWeightedCommand::createPhylipFile() { string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.dist"; outputNames.push_back(phylipFileName); + outputTypes["phylip"].push_back(phylipFileName); ofstream out; m->openOutputFile(phylipFileName, out);