X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;fp=getseqscommand.cpp;h=9bf188db3d25fa4ac16b82973a2802c3b1e6ad75;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/getseqscommand.cpp b/getseqscommand.cpp new file mode 100644 index 0000000..9bf188d --- /dev/null +++ b/getseqscommand.cpp @@ -0,0 +1,935 @@ +/* + * getseqscommand.cpp + * Mothur + * + * Created by Sarah Westcott on 7/8/09. + * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. + * + */ + +#include "getseqscommand.h" +#include "sequence.hpp" +#include "listvector.hpp" + +//********************************************************************************************************************** +vector GetSeqsCommand::setParameters(){ + try { + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist); + CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy); + CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos); + CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string GetSeqsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n"; + helpString += "It outputs a file containing only the sequences in the .accnos file.\n"; + helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n"; + helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n"; + helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n"; + helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\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, "GetSeqsCommand", "getHelpString"); + exit(1); + } +} + +//********************************************************************************************************************** +GetSeqsCommand::GetSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + outputTypes["accnosreport"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +GetSeqsCommand::GetSeqsCommand(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["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + outputTypes["accnosreport"] = tempOutNames; + + //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 = ""; } + + //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("alignreport"); + //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["alignreport"] = 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("accnos"); + //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["accnos"] = inputDir + it->second; } + } + + it = parameters.find("accnos2"); + //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["accnos2"] = inputDir + it->second; } + } + + it = parameters.find("list"); + //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["list"] = 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; } + } + + 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("taxonomy"); + //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["taxonomy"] = inputDir + it->second; } + } + + it = parameters.find("qfile"); + //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["qfile"] = inputDir + it->second; } + } + } + + + //check for required parameters + accnosfile = validParameter.validFile(parameters, "accnos", true); + if (accnosfile == "not open") { abort = true; } + else if (accnosfile == "not found") { + accnosfile = m->getAccnosFile(); + if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); + abort = true; + } + }else { m->setAccnosFile(accnosfile); } + + if (accnosfile2 == "not found") { accnosfile2 = ""; } + + fastafile = validParameter.validFile(parameters, "fasta", true); + if (fastafile == "not open") { fastafile = ""; abort = true; } + else if (fastafile == "not found") { fastafile = ""; } + else { m->setFastaFile(fastafile); } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { namefile = ""; abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } + + alignfile = validParameter.validFile(parameters, "alignreport", true); + if (alignfile == "not open") { abort = true; } + else if (alignfile == "not found") { alignfile = ""; } + + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { m->setListFile(listfile); } + + taxfile = validParameter.validFile(parameters, "taxonomy", true); + if (taxfile == "not open") { taxfile = ""; abort = true; } + else if (taxfile == "not found") { taxfile = ""; } + else { m->setTaxonomyFile(taxfile); } + + qualfile = validParameter.validFile(parameters, "qfile", true); + if (qualfile == "not open") { abort = true; } + else if (qualfile == "not found") { qualfile = ""; } + else { m->setQualFile(qualfile); } + + accnosfile2 = validParameter.validFile(parameters, "accnos2", true); + if (accnosfile2 == "not open") { abort = true; } + else if (accnosfile2 == "not found") { accnosfile2 = ""; } + + + string usedDups = "true"; + string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "true"; usedDups = ""; } + dups = m->isTrue(temp); + + if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; } + + if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } + } + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int GetSeqsCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //get names you want to keep + readAccnos(); + + if (m->control_pressed) { return 0; } + + //read through the correct file and output lines you want to keep + if (namefile != "") { readName(); } + if (fastafile != "") { readFasta(); } + if (groupfile != "") { readGroup(); } + if (alignfile != "") { readAlign(); } + if (listfile != "") { readList(); } + if (taxfile != "") { readTax(); } + if (qualfile != "") { readQual(); } + if (accnosfile2 != "") { compareAccnos(); } + + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + + if (outputNames.size() != 0) { + 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(); + + //set fasta file as new current fastafile + 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); } + } + + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + + itTypes = outputTypes.find("taxonomy"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); } + } + + itTypes = outputTypes.find("qfile"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); } + } + + } + + return 0; + } + + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "execute"); + exit(1); + } +} + +//********************************************************************************************************************** +int GetSeqsCommand::readFasta(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile); + ofstream out; + m->openOutputFile(outputFileName, out); + + + ifstream in; + m->openInputFile(fastafile, in); + string name; + + bool wroteSomething = false; + int selectedCount = 0; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + Sequence currSeq(in); + name = currSeq.getName(); + + if (name != "") { + //if this name is in the accnos file + if (names.count(name) != 0) { + wroteSomething = true; + + currSeq.printSequence(out); + selectedCount++; + } + } + m->gobble(in); + } + in.close(); + out.close(); + + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readFasta"); + exit(1); + } +} +//********************************************************************************************************************** +int GetSeqsCommand::readQual(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" + m->getExtension(qualfile); + ofstream out; + m->openOutputFile(outputFileName, out); + + + ifstream in; + m->openInputFile(qualfile, in); + string name; + + bool wroteSomething = false; + int selectedCount = 0; + + + while(!in.eof()){ + string saveName = ""; + string name = ""; + string scores = ""; + + in >> name; + + if (name.length() != 0) { + saveName = name.substr(1); + while (!in.eof()) { + char c = in.get(); + if (c == 10 || c == 13){ break; } + else { name += c; } + } + m->gobble(in); + } + + while(in){ + char letter= in.get(); + if(letter == '>'){ in.putback(letter); break; } + else{ scores += letter; } + } + + m->gobble(in); + + if (names.count(saveName) != 0) { + wroteSomething = true; + + out << name << endl << scores; + selectedCount++; + } + + m->gobble(in); + } + in.close(); + out.close(); + + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine(); + + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readQual"); + exit(1); + } +} +//********************************************************************************************************************** +int GetSeqsCommand::readList(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(listfile, in); + + bool wroteSomething = false; + int selectedCount = 0; + + while(!in.eof()){ + + selectedCount = 0; + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + //read in list vector + ListVector list(in); + + //make a new list vector + ListVector newList; + newList.setLabel(list.getLabel()); + + //for each bin + for (int i = 0; i < list.getNumBins(); i++) { + + //parse out names that are in accnos file + string binnames = list.get(i); + + string newNames = ""; + while (binnames.find_first_of(',') != -1) { + string name = binnames.substr(0,binnames.find_first_of(',')); + binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length()); + + //if that name is in the .accnos file, add it + if (names.count(name) != 0) { newNames += name + ","; selectedCount++; } + } + + //get last name + if (names.count(binnames) != 0) { newNames += binnames + ","; selectedCount++; } + + //if there are names in this bin add to new list + if (newNames != "") { + newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma + newList.push_back(newNames); + } + } + + //print new listvector + if (newList.getNumBins() != 0) { + wroteSomething = true; + newList.print(out); + } + + m->gobble(in); + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readList"); + exit(1); + } +} +//********************************************************************************************************************** +int GetSeqsCommand::readName(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile); + ofstream out; + m->openOutputFile(outputFileName, out); + + + ifstream in; + m->openInputFile(namefile, in); + string name, firstCol, secondCol; + + bool wroteSomething = false; + int selectedCount = 0; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> firstCol; + in >> secondCol; + + string hold = ""; + if (dups) { hold = secondCol; } + + vector parsedNames; + m->splitAtComma(secondCol, parsedNames); + + vector validSecond; + for (int i = 0; i < parsedNames.size(); i++) { + if (names.count(parsedNames[i]) != 0) { + validSecond.push_back(parsedNames[i]); + } + } + + if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone + for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); } + out << firstCol << '\t' << hold << endl; + wroteSomething = true; + selectedCount += parsedNames.size(); + }else { + selectedCount += validSecond.size(); + + //if the name in the first column is in the set then print it and any other names in second column also in set + if (names.count(firstCol) != 0) { + + wroteSomething = true; + + out << firstCol << '\t'; + + //you know you have at least one valid second since first column is valid + for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } + out << validSecond[validSecond.size()-1] << endl; + + + //make first name in set you come to first column and then add the remaining names to second column + }else { + //you want part of this row + if (validSecond.size() != 0) { + + wroteSomething = true; + + out << validSecond[0] << '\t'; + + //you know you have at least one valid second since first column is valid + for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } + out << validSecond[validSecond.size()-1] << endl; + } + } + } + m->gobble(in); + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readName"); + exit(1); + } +} + +//********************************************************************************************************************** +int GetSeqsCommand::readGroup(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); + ofstream out; + m->openOutputFile(outputFileName, out); + + + ifstream in; + m->openInputFile(groupfile, in); + string name, group; + + bool wroteSomething = false; + int selectedCount = 0; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + + in >> name; //read from first column + in >> group; //read from second column + + //if this name is in the accnos file + if (names.count(name) != 0) { + wroteSomething = true; + + out << name << '\t' << group << endl; + selectedCount++; + } + + m->gobble(in); + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine(); + + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readGroup"); + exit(1); + } +} +//********************************************************************************************************************** +int GetSeqsCommand::readTax(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile); + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(taxfile, in); + string name, tax; + + bool wroteSomething = false; + int selectedCount = 0; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; //read from first column + in >> tax; //read from second column + + //if this name is in the accnos file + if (names.count(name) != 0) { + wroteSomething = true; + + out << name << '\t' << tax << endl; + selectedCount++; + } + + m->gobble(in); + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readTax"); + exit(1); + } +} +//********************************************************************************************************************** +//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name +int GetSeqsCommand::readAlign(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report"; + ofstream out; + m->openOutputFile(outputFileName, out); + + + ifstream in; + m->openInputFile(alignfile, in); + string name, junk; + + bool wroteSomething = false; + int selectedCount = 0; + + //read column headers + for (int i = 0; i < 16; i++) { + if (!in.eof()) { in >> junk; out << junk << '\t'; } + else { break; } + } + out << endl; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + + in >> name; //read from first column + + //if this name is in the accnos file + if (names.count(name) != 0) { + wroteSomething = true; + selectedCount++; + + out << name << '\t'; + + //read rest + for (int i = 0; i < 15; i++) { + if (!in.eof()) { in >> junk; out << junk << '\t'; } + else { break; } + } + out << endl; + + }else {//still read just don't do anything with it + //read rest + for (int i = 0; i < 15; i++) { + if (!in.eof()) { in >> junk; } + else { break; } + } + } + + m->gobble(in); + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readAlign"); + exit(1); + } +} +//********************************************************************************************************************** + +int GetSeqsCommand::readAccnos(){ + try { + + ifstream in; + m->openInputFile(accnosfile, in); + string name; + + while(!in.eof()){ + in >> name; + + names.insert(name); + + m->gobble(in); + } + in.close(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readAccnos"); + exit(1); + } +} +//********************************************************************************************************************** + +int GetSeqsCommand::compareAccnos(){ + try { + + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(accnosfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report"; + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(accnosfile2, in); + string name; + + set namesAccnos2; + set namesDups; + set namesAccnos = names; + + map nameCount; + + if (namefile != "") { + ifstream inName; + m->openInputFile(namefile, inName); + + + while(!inName.eof()){ + + if (m->control_pressed) { inName.close(); return 0; } + + string thisname, repnames; + + inName >> thisname; m->gobble(inName); //read from first column + inName >> repnames; //read from second column + + int num = m->getNumNames(repnames); + nameCount[thisname] = num; + + m->gobble(inName); + } + inName.close(); + } + + while(!in.eof()){ + in >> name; + + if (namesAccnos.count(name) == 0){ //name unique to accnos2 + int pos = name.find_last_of('_'); + string tempName = name; + if (pos != string::npos) { tempName = tempName.substr(pos+1); cout << tempName << endl; } + if (namesAccnos.count(tempName) == 0){ + namesAccnos2.insert(name); + }else { //you are in both so erase + namesAccnos.erase(name); + namesDups.insert(name); + } + }else { //you are in both so erase + namesAccnos.erase(name); + namesDups.insert(name); + } + + m->gobble(in); + } + in.close(); + + out << "Names in both files : " + toString(namesDups.size()) << endl; + m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine(); + + for (set::iterator it = namesDups.begin(); it != namesDups.end(); it++) { + out << (*it); + if (namefile != "") { out << '\t' << nameCount[(*it)]; } + out << endl; + } + + out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl; + m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine(); + + for (set::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) { + out << (*it); + if (namefile != "") { out << '\t' << nameCount[(*it)]; } + out << endl; + } + + out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl; + m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine(); + + for (set::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) { + out << (*it); + if (namefile != "") { out << '\t' << nameCount[(*it)]; } + out << endl; + } + + out.close(); + + outputNames.push_back(outputFileName); outputTypes["accnosreport"].push_back(outputFileName); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "readAccnos"); + exit(1); + } +} + + +//********************************************************************************************************************** +