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Adds merge.count command
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a7d353d
commit b27d5eccf9cbe98edb49140355b488e54e32a723
mothur-westcott
committed
Aug 3, 2016
mothur-westcott
committed
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320 additions
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- +8 −0 Mothur.xcodeproj/project.pbxproj
- +5 −0 source/commandfactory.cpp
- +2 −0 source/commands/helpcommand.cpp
- +226 −0 source/commands/mergecountcommand.cpp
- +48 −0 source/commands/mergecountcommand.hpp
- +5 −0 source/commands/mergegroupscommand.cpp
- +23 −1 source/datastructures/counttable.cpp
- +3 −2 source/datastructures/counttable.h
| @@ -0,0 +1,226 @@ | ||
| +// | ||
| +// mergecountcommand.cpp | ||
| +// Mothur | ||
| +// | ||
| +// Created by Sarah Westcott on 8/3/16. | ||
| +// Copyright © 2016 Schloss Lab. All rights reserved. | ||
| +// | ||
| + | ||
| +#include "mergecountcommand.hpp" | ||
| +#include "counttable.h" | ||
| + | ||
| +//********************************************************************************************************************** | ||
| +vector<string> MergeCountCommand::setParameters(){ | ||
| + try { | ||
| + CommandParameter pcount("count", "InputTypes", "", "", "", "", "","count",false,false,true); parameters.push_back(pcount); | ||
| + CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput); | ||
| + CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed); | ||
| + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); | ||
| + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); | ||
| + | ||
| + vector<string> myArray; | ||
| + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } | ||
| + return myArray; | ||
| + } | ||
| + catch(exception& e) { | ||
| + m->errorOut(e, "MergeCountCommand", "setParameters"); | ||
| + exit(1); | ||
| + } | ||
| +} | ||
| +//********************************************************************************************************************** | ||
| +string MergeCountCommand::getHelpString(){ | ||
| + try { | ||
| + string helpString = ""; | ||
| + helpString += "The merge.count command takes a list of count files separated by dashes and merges them into one file."; | ||
| + helpString += "The merge.count command parameters are count and output."; | ||
| + helpString += "Example merge.count(count=final.count_table-new.count_table, output=complete.count_table)."; | ||
| + helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n"; | ||
| + return helpString; | ||
| + } | ||
| + catch(exception& e) { | ||
| + m->errorOut(e, "MergeCountCommand", "getHelpString"); | ||
| + exit(1); | ||
| + } | ||
| +} | ||
| +//********************************************************************************************************************** | ||
| +MergeCountCommand::MergeCountCommand(){ | ||
| + try { | ||
| + abort = true; calledHelp = true; | ||
| + setParameters(); | ||
| + vector<string> tempOutNames; | ||
| + outputTypes["count"] = tempOutNames; | ||
| + } | ||
| + catch(exception& e) { | ||
| + m->errorOut(e, "MergeCountCommand", "MergeCountCommand"); | ||
| + exit(1); | ||
| + } | ||
| +} | ||
| +//********************************************************************************************************************** | ||
| + | ||
| +MergeCountCommand::MergeCountCommand(string option) { | ||
| + try { | ||
| + abort = false; calledHelp = false; | ||
| + | ||
| + if(option == "help") { | ||
| + help(); | ||
| + abort = true; calledHelp = true; | ||
| + }else if(option == "citation") { citation(); abort = true; calledHelp = true;} | ||
| + else { | ||
| + vector<string> myArray = setParameters(); | ||
| + | ||
| + OptionParser parser(option); | ||
| + map<string,string> parameters = parser.getParameters(); | ||
| + | ||
| + ValidParameters validParameter; | ||
| + | ||
| + //check to make sure all parameters are valid for command | ||
| + for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { | ||
| + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } | ||
| + } | ||
| + | ||
| + //initialize outputTypes | ||
| + vector<string> tempOutNames; | ||
| + outputTypes["count"] = 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 = ""; } | ||
| + | ||
| + string fileList = validParameter.validFile(parameters, "count", false); | ||
| + if(fileList == "not found") { m->mothurOut("[ERROR]: you must enter two or more count file names"); m->mothurOutEndLine(); abort=true; } | ||
| + else{ m->splitAtDash(fileList, fileNames); } | ||
| + | ||
| + //if the user changes the output directory command factory will send this info to us in the output parameter | ||
| + string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found") { outputDir = ""; } | ||
| + | ||
| + | ||
| + numInputFiles = fileNames.size(); | ||
| + ifstream testFile; | ||
| + if(numInputFiles == 0){ | ||
| + m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) + " file names"); m->mothurOutEndLine(); | ||
| + abort=true; | ||
| + } | ||
| + else{ | ||
| + for(int i=0;i<numInputFiles;i++){ | ||
| + if (inputDir != "") { | ||
| + string path = m->hasPath(fileNames[i]); | ||
| + //if the user has not given a path then, add inputdir. else leave path alone. | ||
| + if (path == "") { fileNames[i] = inputDir + fileNames[i]; } | ||
| + } | ||
| + | ||
| + map<string, string> file; file["file"] = fileNames[i]; | ||
| + fileNames[i] = validParameter.validFile(file, "file", true); | ||
| + if(fileNames[i] == "not found"){ abort = true; } | ||
| + } | ||
| + } | ||
| + | ||
| + outputFileName = validParameter.validFile(parameters, "output", false); | ||
| + if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine(); abort=true; } | ||
| + else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); } | ||
| + } | ||
| + | ||
| + } | ||
| + catch(exception& e) { | ||
| + m->errorOut(e, "MergeCountCommand", "MergeCountCommand"); | ||
| + exit(1); | ||
| + } | ||
| +} | ||
| +//********************************************************************************************************************** | ||
| + | ||
| +int MergeCountCommand::execute(){ | ||
| + try { | ||
| + if (abort == true) { if (calledHelp) { return 0; } return 2; } | ||
| + | ||
| + m->mothurRemove(outputFileName); | ||
| + | ||
| + //read headers from each file to confirm all contain groupinfo or all do not | ||
| + //Also collect all group names | ||
| + bool allContainGroups = true; bool allNoGroups = true; | ||
| + set<string> allGroups; | ||
| + for(int i = 0; i < numInputFiles; i++) { | ||
| + | ||
| + if (m->control_pressed) { return 0; } | ||
| + | ||
| + vector<string> thisTablesGroups; | ||
| + CountTable table; | ||
| + bool hasGroups = table.testGroups(fileNames[i], thisTablesGroups); | ||
| + | ||
| + if (hasGroups) { | ||
| + allNoGroups = false; | ||
| + for (int j = 0; j < thisTablesGroups.size(); j++) { allGroups.insert(thisTablesGroups[j]); } | ||
| + }else { allContainGroups = false; } | ||
| + } | ||
| + int numGroups = allGroups.size(); | ||
| + | ||
| + //check to make sure all files are one type - quit if not | ||
| + if (!allContainGroups && !allNoGroups) { m->mothurOut("[ERROR]: your have countfiles that contains group information and count files that do not. These cannot be combined without loss of information, please correct.\n"); m->control_pressed = true; return 0; } | ||
| + | ||
| + if (m->control_pressed) { return 0; } | ||
| + | ||
| + //Create Blank Table - (set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames | ||
| + set<string> seqNames; map<string, string> seqGroup; set<string> g; | ||
| + CountTable completeTable; | ||
| + completeTable.createTable(seqNames, seqGroup, g); | ||
| + | ||
| + //append first one to get headers | ||
| + map<string, int> groupIndex; | ||
| + if (allNoGroups) { m->appendBinaryFiles(fileNames[0], outputFileName); } | ||
| + else { //create groupMap to save time setting abundance vector | ||
| + int count = 0; | ||
| + for (set<string>::iterator it = allGroups.begin(); it != allGroups.end(); it++) { | ||
| + completeTable.addGroup(*it); | ||
| + groupIndex[*it] = count; count++; | ||
| + } | ||
| + } | ||
| + | ||
| + //for each file | ||
| + for(int i = 0; i < numInputFiles; i++) { | ||
| + | ||
| + if (m->control_pressed) { break; } | ||
| + | ||
| + if (allContainGroups) { | ||
| + | ||
| + CountTable table; table.readTable(fileNames[i], true, false); | ||
| + vector<string> groups = table.getNamesOfGroups(); | ||
| + | ||
| + vector<string> seqs = table.getNamesOfSeqs(); | ||
| + for (int j = 0; j < seqs.size(); j++) { | ||
| + if (m->control_pressed) { break; } | ||
| + vector<int> abunds = table.getGroupCounts(seqs[j]); | ||
| + vector<int> newAbunds; newAbunds.resize(numGroups, 0); | ||
| + for (int k = 0; k < abunds.size(); k++) { | ||
| + if (abunds[k] != 0) { //we need to set abundance in vector with all groups | ||
| + //groups and abunds are in matching order. we know all groups are in groupIndex from above. | ||
| + int newIndex = groupIndex[groups[k]]; | ||
| + newAbunds[newIndex] = abunds[k]; | ||
| + } | ||
| + } | ||
| + completeTable.push_back(seqs[j], newAbunds); | ||
| + } | ||
| + } | ||
| + else { m->appendFilesWithoutHeaders(fileNames[i], outputFileName); } //No group info so simple append | ||
| + } | ||
| + | ||
| + if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; } | ||
| + | ||
| + //print new table | ||
| + if (allContainGroups) { completeTable.printTable(outputFileName); } | ||
| + | ||
| + if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; } | ||
| + | ||
| + //update current count file | ||
| + m->setCountTableFile(outputFileName); | ||
| + | ||
| + m->mothurOutEndLine(); | ||
| + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); | ||
| + m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName); | ||
| + m->mothurOutEndLine(); | ||
| + | ||
| + return 0; | ||
| + } | ||
| + catch(exception& e) { | ||
| + m->errorOut(e, "MergeCountCommand", "execute"); | ||
| + exit(1); | ||
| + } | ||
| +} | ||
| +//********************************************************************************************************************** |
| @@ -0,0 +1,48 @@ | ||
| +// | ||
| +// mergecountcommand.hpp | ||
| +// Mothur | ||
| +// | ||
| +// Created by Sarah Westcott on 8/3/16. | ||
| +// Copyright © 2016 Schloss Lab. All rights reserved. | ||
| +// | ||
| + | ||
| +#ifndef mergecountcommand_hpp | ||
| +#define mergecountcommand_hpp | ||
| + | ||
| +#include "command.hpp" | ||
| + | ||
| +class MergeCountCommand : public Command { | ||
| + | ||
| +#ifdef UNIT_TEST | ||
| + //friend class TestMergeCountCommand; | ||
| +#endif | ||
| + | ||
| +public: | ||
| + MergeCountCommand(string); | ||
| + MergeCountCommand(); | ||
| + ~MergeCountCommand() {} | ||
| + | ||
| + vector<string> setParameters(); | ||
| + string getCommandName() { return "merge.count"; } | ||
| + string getCommandCategory() { return "General"; } | ||
| + | ||
| + string getHelpString(); | ||
| + string getOutputPattern(string) { return ""; } | ||
| + string getCitation() { return "http://www.mothur.org/wiki/Merge.count"; } | ||
| + string getDescription() { return "reads count files and combines them into a single count file"; } | ||
| + | ||
| + | ||
| + int execute(); | ||
| + void help() { m->mothurOut(getHelpString()); } | ||
| + | ||
| +private: | ||
| + | ||
| + bool abort; | ||
| + string outputDir, inputDir, countfile, output, outputFileName; | ||
| + vector<string> outputNames, fileNames; | ||
| + int numInputFiles; | ||
| + | ||
| +}; | ||
| + | ||
| + | ||
| +#endif /* mergecountcommand_hpp */ |
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