X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countgroupscommand.cpp;h=716dc90693969140d3af32403d3818c04224d7f9;hb=a9dbc22713bfc056a797361dd757b1a5c98e1c01;hp=0c03882a459135afaad797728f2ed268b17c9abb;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp index 0c03882..716dc90 100644 --- a/countgroupscommand.cpp +++ b/countgroupscommand.cpp @@ -16,6 +16,7 @@ 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 pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); 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); @@ -34,7 +35,7 @@ vector CountGroupsCommand::setParameters(){ 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"; @@ -114,6 +115,14 @@ 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; } + } } @@ -138,9 +147,23 @@ 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 +171,11 @@ 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; + } } } } @@ -170,7 +197,7 @@ int CountGroupsCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } //get groups you want to remove - if (accnosfile != "") { readAccnos(); } + if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); } if (groupfile != "") { GroupMap groupMap(groupfile); @@ -182,9 +209,36 @@ int CountGroupsCommand::execute(){ vector nameGroups = groupMap.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 = groupMap.getNumSeqs(Groups[i]); + total += num; + m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine(); } + + m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine(); + } + + if (m->control_pressed) { return 0; } + + if (countfile != "") { + CountTable ct; + ct.readTable(countfile); + + //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++) { + int num = ct.getGroupCount(Groups[i]); + total += num; + m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine(); + } + + m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine(); } if (m->control_pressed) { return 0; } @@ -193,10 +247,15 @@ int CountGroupsCommand::execute(){ InputData input(sharedfile, "sharedfile"); vector lookup = input.getSharedRAbundVectors(); + 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]; - } + } + + m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine(); } return 0; @@ -208,31 +267,5 @@ int CountGroupsCommand::execute(){ } } //********************************************************************************************************************** -void CountGroupsCommand::readAccnos(){ - try { - Groups.clear(); - - ifstream in; - m->openInputFile(accnosfile, in); - string name; - - while(!in.eof()){ - in >> name; - - Groups.push_back(name); - - m->gobble(in); - } - in.close(); - - m->setGroups(Groups); - - } - catch(exception& e) { - m->errorOut(e, "CountGroupsCommand", "readAccnos"); - exit(1); - } -} -//**********************************************************************************************************************