From d0cceb86216f1174afa51582a51490294912b00e Mon Sep 17 00:00:00 2001 From: westcott Date: Fri, 16 Sep 2011 14:17:47 +0000 Subject: [PATCH] modified split.groups to use sequenceParser --- splitgroupscommand.cpp | 180 ++++++++--------------------------------- splitgroupscommand.h | 8 +- 2 files changed, 33 insertions(+), 155 deletions(-) diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp index 530df68..113439c 100644 --- a/splitgroupscommand.cpp +++ b/splitgroupscommand.cpp @@ -9,6 +9,7 @@ #include "splitgroupscommand.h" #include "sharedutilities.h" +#include "sequenceparser.h" //********************************************************************************************************************** vector SplitGroupCommand::setParameters(){ @@ -164,16 +165,40 @@ int SplitGroupCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } - groupMap = new GroupMap(groupfile); - groupMap->readMap(); + SequenceParser* parser; - vector namesGroups = groupMap->getNamesOfGroups(); + 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); - if (namefile != "") { readNames(); } - splitFasta(); + string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile)); - delete groupMap; + 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; } @@ -200,147 +225,6 @@ int SplitGroupCommand::execute(){ exit(1); } } -/**********************************************************************************************************************/ -int SplitGroupCommand::readNames() { - try { - //open input file - ifstream in; - m->openInputFile(namefile, in); - - while (!in.eof()) { - if (m->control_pressed) { break; } - - string firstCol, secondCol; - in >> firstCol >> secondCol; m->gobble(in); - - vector names; - m->splitAtComma(secondCol, names); - - nameMap[firstCol] = names; - } - in.close(); - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "SplitGroupCommand", "readNames"); - exit(1); - } -} - -/**********************************************************************************************************************/ -int SplitGroupCommand::splitFasta() { - try { - - string filerootFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)); - string filerootName = outputDir + m->getRootName(m->getSimpleName(namefile)); - ofstream* temp; - ofstream* temp2; - map filehandles; - map::iterator it3; - - for (int i=0; iopenOutputFile(filerootFasta + Groups[i] + ".fasta", *(filehandles[Groups[i]+"fasta"])); - outputNames.push_back(filerootFasta + Groups[i] + ".fasta"); outputTypes["fasta"].push_back(filerootFasta + Groups[i] + ".fasta"); - - if (namefile != "") { - temp2 = new ofstream; - filehandles[Groups[i]+"name"] = temp2; - m->openOutputFile(filerootName + Groups[i] + ".names", *(filehandles[Groups[i]+"name"])); - outputNames.push_back(filerootName + Groups[i] + ".names"); outputTypes["name"].push_back(filerootFasta + Groups[i] + ".names"); - } - } - - //open input file - ifstream in; - m->openInputFile(fastafile, in); - - while (!in.eof()) { - if (m->control_pressed) { break; } - - Sequence seq(in); m->gobble(in); - - if (seq.getName() != "") { - - itNames = nameMap.find(seq.getName()); - - if (itNames == nameMap.end()) { - if (namefile != "") { m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine(); } - else { //no names file given - string group = groupMap->getGroup(seq.getName()); - - if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want - seq.printSequence(*(filehandles[group+"fasta"])); - }else if(group == "not found") { - m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine(); - } - } - }else{ - vector names = itNames->second; - map group2Names; - map::iterator it; - - for (int i = 0; i < names.size(); i++) { //build strings for new group names file, will select rep below - string group = groupMap->getGroup(names[i]); - - if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want - it = group2Names.find(group); - if (it == group2Names.end()) { - group2Names[group] = names[i] + ","; - }else{ - group2Names[group] += names[i] + ","; - } - }else if(group == "not found") { - m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine(); - } - } - - for (map::iterator itGroups = group2Names.begin(); itGroups != group2Names.end(); itGroups++) { - //edit names string, by grabbing the first guy as the rep and removing the last comma - string newNames = itGroups->second; - newNames = newNames.substr(0, newNames.length()-1); - string repName = ""; - - int pos = newNames.find_first_of(','); - if (pos == newNames.npos) { //only one sequence so it represents itself - repName = newNames; - }else{ - repName = newNames.substr(0, pos); - } - - *(filehandles[itGroups->first+"name"]) << repName << '\t' << newNames << endl; - *(filehandles[itGroups->first+"fasta"]) << ">" << repName << endl << seq.getAligned() << endl; - } - } - } - } - - in.close(); - - for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { - (*(filehandles[it3->first])).close(); - delete it3->second; - } - - vector newOutputNames; - //remove blank files - for (int i = 0; i < outputNames.size(); i++) { - if (m->isBlank(outputNames[i])) { - m->mothurRemove(outputNames[i]); - }else { newOutputNames.push_back(outputNames[i]); } - } - outputNames = newOutputNames; - - return 0; +//********************************************************************************************************************** - } - catch(exception& e) { - m->errorOut(e, "SplitGroupCommand", "splitFasta"); - exit(1); - } -} -/**********************************************************************************************************************/ diff --git a/splitgroupscommand.h b/splitgroupscommand.h index f8bdca1..a6b8854 100644 --- a/splitgroupscommand.h +++ b/splitgroupscommand.h @@ -39,14 +39,8 @@ public: void help() { m->mothurOut(getHelpString()); } private: - int readNames(); - int splitFasta(); - vector outputNames; - map > nameMap; - map >::iterator itNames; - GroupMap* groupMap; - + string outputDir, namefile, groupfile, groups, fastafile; vector Groups; bool abort; -- 2.39.2