X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitgroupscommand.cpp;fp=splitgroupscommand.cpp;h=26716554decad148623563d4b120148325b7477a;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp new file mode 100644 index 0000000..2671655 --- /dev/null +++ b/splitgroupscommand.cpp @@ -0,0 +1,235 @@ +/* + * splitgroupscommand.cpp + * Mothur + * + * Created by westcott on 9/20/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "splitgroupscommand.h" +#include "sharedutilities.h" +#include "sequenceparser.h" + +//********************************************************************************************************************** +vector SplitGroupCommand::setParameters(){ + try { + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup); + 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); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SplitGroupCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string SplitGroupCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The split.group command reads a group file, and parses your fasta and names files by groups. \n"; + helpString += "The split.group command parameters are fasta, name, group and groups.\n"; + helpString += "The fasta and group parameters are required.\n"; + helpString += "The groups parameter allows you to select groups to create files for. \n"; + helpString += "For example if you set groups=A-B-C, you will get a .A.fasta, .A.names, .B.fasta, .B.names, .C.fasta, .C.names files. \n"; + helpString += "If you want .fasta and .names files for all groups, set groups=all. \n"; + helpString += "The split.group command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n"; + helpString += "Example: split.group(fasta=abrecovery.fasta, group=abrecovery.groups).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "SplitGroupCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +SplitGroupCommand::SplitGroupCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "SplitGroupCommand", "SplitGroupCommand"); + exit(1); + } +} +//********************************************************************************************************************** +SplitGroupCommand::SplitGroupCommand(string option) { + try { + abort = false; calledHelp = false; + + //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(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("group"); + //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["group"] = inputDir + it->second; } + } + + it = parameters.find("fasta"); + //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["fasta"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //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["name"] = inputDir + it->second; } + } + + } + + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { namefile = ""; abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } + + fastafile = validParameter.validFile(parameters, "fasta", true); + if (fastafile == "not open") { abort = true; } + else if (fastafile == "not found") { + fastafile = m->getFastaFile(); + if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setFastaFile(fastafile); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { groupfile = ""; abort = true; } + else if (groupfile == "not found") { + 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 and the group parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setGroupFile(groupfile); } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { m->splitAtDash(groups, Groups); } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(groupfile); } + + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } + + } + catch(exception& e) { + m->errorOut(e, "SplitGroupCommand", "SplitAbundCommand"); + exit(1); + } +} +//********************************************************************************************************************** +int SplitGroupCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + SequenceParser* parser; + + if (namefile == "") { parser = new SequenceParser(groupfile, fastafile); } + else { parser = new SequenceParser(groupfile, fastafile, namefile); } + + if (m->control_pressed) { delete parser; return 0; } + + vector namesGroups = parser->getNamesOfGroups(); + SharedUtil util; util.setGroups(Groups, namesGroups); + + string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile)); + + m->mothurOutEndLine(); + for (int i = 0; i < Groups.size(); i++) { + + m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine(); + + string newFasta = fastafileRoot + Groups[i] + ".fasta"; + string newName = namefileRoot + Groups[i] + ".names"; + + parser->getSeqs(Groups[i], newFasta, false); + outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta); + if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + if (namefile != "") { + parser->getNameMap(Groups[i], newName); + outputNames.push_back(newName); outputTypes["name"].push_back(newName); + } + + if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + } + + delete parser; + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + itTypes = outputTypes.find("name"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } + } + + 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; + } + catch(exception& e) { + m->errorOut(e, "SplitGroupCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** + +