X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=5ae8da588ba4a6d36b6658527d8cd12e208c50c4;hb=8d341208b0cd0c7a4ff8b77c6b164e06f2f39610;hp=02461365b505bdea22cc977594fc1341ca7bac46;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp index 0246136..5ae8da5 100644 --- a/getsharedotucommand.cpp +++ b/getsharedotucommand.cpp @@ -13,15 +13,15 @@ //********************************************************************************************************************** vector GetSharedOTUCommand::setParameters(){ try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup); - CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist); - CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique); - CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(plist); + CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter punique("unique", "String", "", "", "", "", "","",false,false,true); parameters.push_back(punique); + CommandParameter pshared("shared", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pshared); + 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); } @@ -46,8 +46,8 @@ string GetSharedOTUCommand::getHelpString(){ helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n"; helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n"; helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n"; - helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n"; - helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n"; + helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n"; + helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n"; helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n"; helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n"; helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n"; @@ -59,6 +59,23 @@ string GetSharedOTUCommand::getHelpString(){ } } //********************************************************************************************************************** +string GetSharedOTUCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],[distance],[group],shared.fasta"; } + else if (type == "accnos") { pattern = "[filename],[distance],[group],accnos"; } + else if (type == "sharedseqs") { pattern = "[filename],[distance],[group],shared.seqs"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** GetSharedOTUCommand::GetSharedOTUCommand(){ try { abort = true; calledHelp = true; @@ -182,7 +199,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { else { userGroups = "unique." + groups; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } @@ -191,7 +208,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { else { userGroups = groups; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); unique = false; } @@ -221,7 +238,7 @@ int GetSharedOTUCommand::execute(){ if (m->control_pressed) { delete groupMap; return 0; } if (Groups.size() == 0) { - Groups = groupMap->namesOfGroups; + Groups = groupMap->getNamesOfGroups(); //make string for outputfile name userGroups = "unique."; @@ -230,7 +247,9 @@ int GetSharedOTUCommand::execute(){ }else{ //sanity check for group names SharedUtil util; - util.setGroups(Groups, groupMap->namesOfGroups); + vector namesOfGroups = groupMap->getNamesOfGroups(); + util.setGroups(Groups, namesOfGroups); + groupMap->setNamesOfGroups(namesOfGroups); } //put groups in map to find easier @@ -325,7 +344,7 @@ int GetSharedOTUCommand::execute(){ //reset groups parameter - m->Groups.clear(); + m->clearGroups(); if (lastlist != NULL) { delete lastlist; } @@ -369,11 +388,13 @@ int GetSharedOTUCommand::process(ListVector* shared) { string outputFileNames; if (outputDir == "") { outputDir += m->hasPath(listfile); } - if (output != "accnos") { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs"; - }else { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos"; - } + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[distance]"] = shared->getLabel(); + variables["[group]"] = userGroups; + if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); } + else { outputFileNames = getOutputFileName("accnos", variables); } + m->openOutputFile(outputFileNames, outNames); bool wroteSomething = false; @@ -392,10 +413,11 @@ int GetSharedOTUCommand::process(ListVector* shared) { vector namesOfSeqsInThisBin; - string names = shared->get(i); - while ((names.find_first_of(',') != -1)) { - string name = names.substr(0,names.find_first_of(',')); - names = names.substr(names.find_first_of(',')+1, names.length()); + string names = shared->get(i); + vector binNames; + m->splitAtComma(names, binNames); + for(int j = 0; j < binNames.size(); j++) { + string name = binNames[j]; //find group string seqGroup = groupMap->getGroup(name); @@ -411,20 +433,6 @@ int GetSharedOTUCommand::process(ListVector* shared) { else { atLeastOne[seqGroup]++; } } - //get last name - string seqGroup = groupMap->getGroup(names); - if (output != "accnos") { - namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1))); - }else { namesOfSeqsInThisBin.push_back(names); } - - if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); } - - //is this seq in one of hte groups we care about - it = groupFinder.find(seqGroup); - if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want - else { atLeastOne[seqGroup]++; } - - //make sure you have at least one seq from each group you want bool sharedByAll = true; map::iterator it2; @@ -479,7 +487,8 @@ int GetSharedOTUCommand::process(ListVector* shared) { //if fasta file provided output new fasta file if ((fastafile != "") && wroteSomething) { if (outputDir == "") { outputDir += m->hasPath(fastafile); } - string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta"; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string outputFileFasta = getOutputFileName("fasta", variables); ofstream outFasta; m->openOutputFile(outputFileFasta, outFasta); outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);