X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.cpp;h=0c867e35f730cc8e72c66153b14c23b5f54ce6f3;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=c4ef741f80c22bc784df4e6916f4a214fb2feacd;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp index c4ef741..0c867e3 100644 --- a/binsequencecommand.cpp +++ b/binsequencecommand.cpp @@ -50,6 +50,26 @@ string BinSeqCommand::getHelpString(){ } } //********************************************************************************************************************** +string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "fasta") { outputFileName = "fasta"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "BinSeqCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** BinSeqCommand::BinSeqCommand(){ try { abort = true; calledHelp = true; @@ -138,6 +158,7 @@ BinSeqCommand::BinSeqCommand(string option) { else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } } else if (fastafile == "not open") { abort = true; } + else { m->setFastaFile(fastafile); } listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not found") { @@ -146,6 +167,7 @@ BinSeqCommand::BinSeqCommand(string option) { else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; } } else if (listfile == "not open") { listfile = ""; abort = true; } + else { m->setListFile(listfile); } //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"){ @@ -165,12 +187,19 @@ BinSeqCommand::BinSeqCommand(string option) { } namesfile = validParameter.validFile(parameters, "name", true); - if (namesfile == "not open") { abort = true; } + if (namesfile == "not open") { namesfile = ""; abort = true; } else if (namesfile == "not found") { namesfile = ""; } + else { m->setNameFile(namesfile); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } + + if (namesfile == ""){ + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } } } @@ -217,12 +246,12 @@ int BinSeqCommand::execute(){ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } + if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } if(allLines == 1 || labels.count(list->getLabel()) == 1){ error = process(list); - if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } + if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -235,7 +264,7 @@ int BinSeqCommand::execute(){ list = input->getListVector(lastLabel); error = process(list); - if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } + if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -250,7 +279,7 @@ int BinSeqCommand::execute(){ list = input->getListVector(); } - if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } + if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } //output error messages about any remaining user labels set::iterator it; @@ -271,7 +300,7 @@ int BinSeqCommand::execute(){ list = input->getListVector(lastLabel); error = process(list); - if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } + if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; } delete list; } @@ -280,7 +309,7 @@ int BinSeqCommand::execute(){ delete fasta; if (groupfile != "") { delete groupMap; } - if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -333,79 +362,48 @@ void BinSeqCommand::readNamesFile() { //return 1 if error, 0 otherwise int BinSeqCommand::process(ListVector* list) { try { - string binnames, name, sequence; - - string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta"; - m->openOutputFile(outputFileName, out); - - //save to output list of output file names - outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); - - m->mothurOut(list->getLabel()); m->mothurOutEndLine(); - - //for each bin in the list vector - for (int i = 0; i < list->size(); i++) { - - if (m->control_pressed) { return 1; } - - binnames = list->get(i); - while (binnames.find_first_of(',') != -1) { - name = binnames.substr(0,binnames.find_first_of(',')); - binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length()); - - //do work for that name - sequence = fasta->getSequence(name); - if (sequence != "not found") { - //if you don't have groups - if (groupfile == "") { - name = name + "\t" + toString(i+1); - out << ">" << name << endl; - out << sequence << endl; - }else {//if you do have groups - string group = groupMap->getGroup(name); - if (group == "not found") { - m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine(); - return 1; - }else{ - name = name + "\t" + group + "\t" + toString(i+1); - out << ">" << name << endl; - out << sequence << endl; - } - } - }else { - m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine(); - return 1; - } - - } - - //get last name - sequence = fasta->getSequence(binnames); - if (sequence != "not found") { - //if you don't have groups - if (groupfile == "") { - binnames = binnames + "\t" + toString(i+1); - out << ">" << binnames << endl; - out << sequence << endl; - }else {//if you do have groups - string group = groupMap->getGroup(binnames); - if (group == "not found") { - m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine(); - return 1; - }else{ - binnames = binnames + "\t" + group + "\t" + toString(i+1); - out << ">" << binnames << endl; - out << sequence << endl; - } - } - }else { - m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine(); - return 1; - } - } - - out.close(); - return 0; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta"); + m->openOutputFile(outputFileName, out); + outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); + + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); + + //for each bin in the list vector + for (int i = 0; i < list->size(); i++) { + + if (m->control_pressed) { return 1; } + + string binnames = list->get(i); + vector names; + m->splitAtComma(binnames, names); + for (int j = 0; j < names.size(); j++) { + string name = names[j]; + + //do work for that name + string sequence = fasta->getSequence(name); + if (sequence != "not found") { + //if you don't have groups + if (groupfile == "") { + name = name + "\t" + toString(i+1); + out << ">" << name << endl; + out << sequence << endl; + }else {//if you do have groups + string group = groupMap->getGroup(name); + if (group == "not found") { + m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine(); + return 1; + }else{ + name = name + "\t" + group + "\t" + toString(i+1); + out << ">" << name << endl; + out << sequence << endl; + } + } + }else { m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine(); return 1; } + } + } + + out.close(); + return 0; } catch(exception& e) {