X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitgroupscommand.cpp;fp=splitgroupscommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=26716554decad148623563d4b120148325b7477a;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp deleted file mode 100644 index 2671655..0000000 --- a/splitgroupscommand.cpp +++ /dev/null @@ -1,235 +0,0 @@ -/* - * 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); - } -} -//********************************************************************************************************************** - -