X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=9beca6aa96f75a58891b5326b5cbd94209701656;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=06e199f7a93c96e71ba5cb15f1cafd21c8ca2d8e;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp index 06e199f..9beca6a 100644 --- a/getsharedotucommand.cpp +++ b/getsharedotucommand.cpp @@ -8,6 +8,7 @@ */ #include "getsharedotucommand.h" +#include "sharedutilities.h" //********************************************************************************************************************** vector GetSharedOTUCommand::setParameters(){ @@ -45,8 +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"; @@ -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 { @@ -181,7 +205,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { else { userGroups = "unique." + groups; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } @@ -190,7 +214,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { else { userGroups = groups; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); unique = false; } @@ -220,12 +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 @@ -261,7 +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; } @@ -320,11 +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 = ""; @@ -365,9 +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); @@ -376,7 +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; @@ -454,7 +484,7 @@ 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 = ""; @@ -474,7 +504,7 @@ 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);