X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=1b69a25d4af7e638dbf48a64baec2390f37dcfec;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=f12b1cd19a4a6a1f5c0c61074d4dc22e68aac6dd;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp index f12b1cd..1b69a25 100644 --- a/getsharedotucommand.cpp +++ b/getsharedotucommand.cpp @@ -8,6 +8,7 @@ */ #include "getsharedotucommand.h" +#include "sharedutilities.h" //********************************************************************************************************************** vector GetSharedOTUCommand::setParameters(){ @@ -45,11 +46,11 @@ 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\n"; + helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n"; return helpString; } catch(exception& e) { @@ -57,6 +58,29 @@ string GetSharedOTUCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string GetSharedOTUCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //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 == "fasta") { outputFileName = "shared.fasta"; } + else if (type == "accnos") { outputFileName = "accnos"; } + else if (type == "sharedseqs") { outputFileName = "shared.seqs"; } + 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, "GetSharedOTUCommand", "getOutputFileNameTag"); + exit(1); + } +} + //********************************************************************************************************************** GetSharedOTUCommand::GetSharedOTUCommand(){ try { @@ -82,6 +106,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -147,7 +172,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); abort = true; } - }else { format = "list"; } + }else { format = "list"; m->setListFile(listfile); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } @@ -158,7 +183,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setGroupFile(groupfile); } if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; } @@ -180,7 +205,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { else { userGroups = "unique." + groups; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } @@ -189,14 +214,14 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { else { userGroups = groups; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); unique = false; } fastafile = validParameter.validFile(parameters, "fasta", true); if (fastafile == "not open") { abort = true; } else if (fastafile == "not found") { fastafile = ""; } - + else { m->setFastaFile(fastafile); } } } @@ -219,12 +244,18 @@ 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."; for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; } userGroups = userGroups.substr(0, userGroups.length()-1); + }else{ + //sanity check for group names + SharedUtil util; + vector namesOfGroups = groupMap->getNamesOfGroups(); + util.setGroups(Groups, namesOfGroups); + groupMap->setNamesOfGroups(namesOfGroups); } //put groups in map to find easier @@ -260,7 +291,7 @@ int GetSharedOTUCommand::execute(){ if (m->control_pressed) { if (lastlist != NULL) { delete lastlist; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); delete groupMap; return 0; } @@ -319,11 +350,11 @@ int GetSharedOTUCommand::execute(){ //reset groups parameter - m->Groups.clear(); + m->clearGroups(); if (lastlist != NULL) { delete lastlist; } - if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; } //set fasta file as new current fastafile string current = ""; @@ -364,9 +395,9 @@ int GetSharedOTUCommand::process(ListVector* shared) { if (outputDir == "") { outputDir += m->hasPath(listfile); } if (output != "accnos") { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs"; + outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs"); }else { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos"; + outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos"); } m->openOutputFile(outputFileNames, outNames); @@ -375,7 +406,7 @@ int GetSharedOTUCommand::process(ListVector* shared) { //go through each bin, find out if shared for (int i = 0; i < shared->getNumBins(); i++) { - if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; } + if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; } bool uniqueOTU = true; @@ -386,10 +417,11 @@ 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); @@ -405,20 +437,6 @@ 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; @@ -453,7 +471,7 @@ int GetSharedOTUCommand::process(ListVector* shared) { outNames.close(); if (!wroteSomething) { - remove(outputFileNames.c_str()); + m->mothurRemove(outputFileNames); string outputString = "\t" + toString(num) + " - No otus shared by groups"; string groupString = ""; @@ -473,7 +491,7 @@ 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"; + string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("fasta"); ofstream outFasta; m->openOutputFile(outputFileFasta, outFasta); outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);