X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;fp=getseqscommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=9bf188db3d25fa4ac16b82973a2802c3b1e6ad75;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/getseqscommand.cpp b/getseqscommand.cpp deleted file mode 100644 index 9bf188d..0000000 --- a/getseqscommand.cpp +++ /dev/null @@ -1,935 +0,0 @@ -/* - * 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); - } -} - - -//********************************************************************************************************************** -