X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=countgroupscommand.cpp;h=ce3358ef43b9cee9d7887314fb0378cb203b7ebe;hp=ccf8988e39308fd2816f6eb0a6ff0454ab944d19;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96 diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp index ccf8988..ce3358e 100644 --- a/countgroupscommand.cpp +++ b/countgroupscommand.cpp @@ -14,12 +14,13 @@ //********************************************************************************************************************** vector CountGroupsCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared); - CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup); - CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos); - 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 pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pshared); + CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pgroup); + CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pcount); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos); + 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); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -31,10 +32,25 @@ vector CountGroupsCommand::setParameters(){ } } //********************************************************************************************************************** +string CountGroupsCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "summary") { pattern = "[filename],count.summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "PrimerDesignCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** string CountGroupsCommand::getHelpString(){ try { string helpString = ""; - helpString += "The count.groups command counts sequences from a specific group or set of groups from the following file types: group or shared file.\n"; + helpString += "The count.groups command counts sequences from a specific group or set of groups from the following file types: group, count or shared file.\n"; helpString += "The count.groups command parameters are accnos, group, shared and groups. You must provide a group or shared file.\n"; helpString += "The accnos parameter allows you to provide a file containing the list of groups.\n"; helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n"; @@ -54,6 +70,8 @@ CountGroupsCommand::CountGroupsCommand(){ try { abort = true; calledHelp = true; setParameters(); + vector tempOutNames; + outputTypes["summary"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand"); @@ -114,8 +132,18 @@ CountGroupsCommand::CountGroupsCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["shared"] = inputDir + it->second; } } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } } + vector tempOutNames; + outputTypes["summary"] = tempOutNames; //check for required parameters accnosfile = validParameter.validFile(parameters, "accnos", true); @@ -138,9 +166,23 @@ CountGroupsCommand::CountGroupsCommand(string option) { groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { groupfile = ""; abort = true; } else if (groupfile == "not found") { groupfile = ""; } - else { m->setGroupFile(groupfile); } + else { m->setGroupFile(groupfile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { countfile = ""; abort = true; } + else if (countfile == "not found") { countfile = ""; } + else { + m->setCountTableFile(countfile); + CountTable ct; + if (!ct.testGroups(countfile)) { m->mothurOut("[ERROR]: Your count file does not have any group information, aborting."); m->mothurOutEndLine(); abort=true; } + } + + if ((groupfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true; + } + - if ((sharedfile == "") && (groupfile == "")) { + if ((sharedfile == "") && (groupfile == "") && (countfile == "")) { //give priority to shared, then group sharedfile = m->getSharedFile(); if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } @@ -148,7 +190,11 @@ CountGroupsCommand::CountGroupsCommand(string option) { groupfile = m->getGroupFile(); if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); } else { - m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true; + countfile = m->getCountTableFile(); + if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current groupfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true; + } } } } @@ -173,6 +219,15 @@ int CountGroupsCommand::execute(){ if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); } if (groupfile != "") { + map variables; + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)); + string outputFileName = getOutputFileName("summary", variables); + outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName); + ofstream out; + m->openOutputFile(outputFileName, out); + GroupMap groupMap(groupfile); groupMap.readMap(); @@ -182,9 +237,48 @@ int CountGroupsCommand::execute(){ vector nameGroups = groupMap.getNamesOfGroups(); util.setGroups(Groups, nameGroups); + int total = 0; + for (int i = 0; i < Groups.size(); i++) { + int num = groupMap.getNumSeqs(Groups[i]); + total += num; + m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine(); + out << Groups[i] << '\t' << num << endl; + } + out.close(); + m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine(); + } + + if (m->control_pressed) { return 0; } + + if (countfile != "") { + map variables; + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(countfile); } + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile)); + string outputFileName = getOutputFileName("summary", variables); + outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName); + ofstream out; + m->openOutputFile(outputFileName, out); + + CountTable ct; + ct.readTable(countfile, true, false); + + //make sure groups are valid + //takes care of user setting groupNames that are invalid or setting groups=all + SharedUtil util; + vector nameGroups = ct.getNamesOfGroups(); + util.setGroups(Groups, nameGroups); + + int total = 0; for (int i = 0; i < Groups.size(); i++) { - m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine(); + int num = ct.getGroupCount(Groups[i]); + total += num; + m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine(); + out << Groups[i] << '\t' << num << endl; } + out.close(); + + m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine(); } if (m->control_pressed) { return 0; } @@ -193,12 +287,33 @@ int CountGroupsCommand::execute(){ InputData input(sharedfile, "sharedfile"); vector lookup = input.getSharedRAbundVectors(); + map variables; + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(countfile); } + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile)); + string outputFileName = getOutputFileName("summary", variables); + outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName); + ofstream out; + m->openOutputFile(outputFileName, out); + + int total = 0; for (int i = 0; i < lookup.size(); i++) { - m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + "."); m->mothurOutEndLine(); + int num = lookup[i]->getNumSeqs(); + total += num; + m->mothurOut(lookup[i]->getGroup() + " contains " + toString(num) + "."); m->mothurOutEndLine(); delete lookup[i]; - } + out << lookup[i]->getGroup() << '\t' << num << endl; + } + out.close(); + + m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine(); } - + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + return 0; }