X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=b48ba28709acfb2b0f1355743c5a860cee1c8529;hb=134a9c1275862a6b3ea10a2c0f11965c0a535854;hp=d63dc79974ac007f504f7f1928ed8d0f031dcfe3;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git diff --git a/getseqscommand.cpp b/getseqscommand.cpp index d63dc79..b48ba28 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -12,17 +12,69 @@ #include "listvector.hpp" //********************************************************************************************************************** - -GetSeqsCommand::GetSeqsCommand(string option){ +vector GetSeqsCommand::getValidParameters(){ + try { + string Array[] = {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +GetSeqsCommand::GetSeqsCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["list"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetSeqsCommand::getRequiredParameters(){ + try { + string Array[] = {"accnos"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetSeqsCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +GetSeqsCommand::GetSeqsCommand(string option) { try { abort = false; - + //allow user to run help if(option == "help") { help(); abort = true; } else { //valid paramters for this command - string Array[] = {"fasta","name", "group", "alignreport", "accnos", "list","outputdir","inputdir"}; + string Array[] = {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -36,6 +88,15 @@ GetSeqsCommand::GetSeqsCommand(string option){ 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; + //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 = ""; } @@ -47,7 +108,7 @@ GetSeqsCommand::GetSeqsCommand(string option){ it = parameters.find("alignreport"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -55,7 +116,7 @@ GetSeqsCommand::GetSeqsCommand(string option){ it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -63,7 +124,7 @@ GetSeqsCommand::GetSeqsCommand(string option){ it = parameters.find("accnos"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -71,7 +132,7 @@ GetSeqsCommand::GetSeqsCommand(string option){ it = parameters.find("list"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -79,7 +140,7 @@ GetSeqsCommand::GetSeqsCommand(string option){ it = parameters.find("name"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -87,17 +148,25 @@ GetSeqsCommand::GetSeqsCommand(string option){ it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } + } } //check for required parameters accnosfile = validParameter.validFile(parameters, "accnos", true); if (accnosfile == "not open") { abort = true; } - else if (accnosfile == "not found") { accnosfile = ""; mothurOut("You must provide an accnos file."); mothurOutEndLine(); abort = true; } + else if (accnosfile == "not found") { accnosfile = ""; m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; } fastafile = validParameter.validFile(parameters, "fasta", true); if (fastafile == "not open") { abort = true; } @@ -119,17 +188,23 @@ GetSeqsCommand::GetSeqsCommand(string option){ if (listfile == "not open") { abort = true; } else if (listfile == "not found") { listfile = ""; } - if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; } + taxfile = validParameter.validFile(parameters, "taxonomy", true); + if (taxfile == "not open") { abort = true; } + else if (taxfile == "not found") { taxfile = ""; } - int okay = 2; - if (outputDir != "") { okay++; } + string usedDups = "true"; + string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; } + dups = m->isTrue(temp); - if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; } + if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; } + + if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; } + } } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "GetSeqsCommand"); + m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand"); exit(1); } } @@ -137,15 +212,16 @@ GetSeqsCommand::GetSeqsCommand(string option){ void GetSeqsCommand::help(){ try { - mothurOut("The get.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n"); - mothurOut("It outputs a file containing only the sequences in the .accnos file.\n"); - mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list and alignreport. You must provide accnos and one of the other parameters.\n"); - mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n"); - mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n"); - mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); + m->mothurOut("The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy or alignreport file.\n"); + m->mothurOut("It outputs a file containing only the sequences in the .accnos file.\n"); + m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, alignreport and dups. You must provide accnos and at least one of the other parameters.\n"); + m->mothurOut("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"); + m->mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n"); + m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "help"); + m->errorOut(e, "GetSeqsCommand", "help"); exit(1); } } @@ -160,80 +236,99 @@ int GetSeqsCommand::execute(){ //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(); } - else if (namefile != "") { readName(); } - else if (groupfile != "") { readGroup(); } - else if (alignfile != "") { readAlign(); } - else if (listfile != "") { readList(); } + if (groupfile != "") { readGroup(); } + if (alignfile != "") { readAlign(); } + if (listfile != "") { readList(); } + if (taxfile != "") { readTax(); } + + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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(); + } return 0; } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "execute"); + m->errorOut(e, "GetSeqsCommand", "execute"); exit(1); } } //********************************************************************************************************************** -void GetSeqsCommand::readFasta(){ +int GetSeqsCommand::readFasta(){ try { - if (outputDir == "") { outputDir += hasPath(fastafile); } - string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); + ifstream in; - openInputFile(fastafile, in); + m->openInputFile(fastafile, in); string name; bool wroteSomething = false; while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + Sequence currSeq(in); name = currSeq.getName(); if (name != "") { //if this name is in the accnos file - if (names.count(name) == 1) { + if (names.count(name) != 0) { wroteSomething = true; currSeq.printSequence(out); - - names.erase(name); } } - gobble(in); + m->gobble(in); } in.close(); out.close(); - if (wroteSomething == false) { - mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine(); - remove(outputFileName.c_str()); - } + 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); + + return 0; } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "readFasta"); + m->errorOut(e, "GetSeqsCommand", "readFasta"); exit(1); } } //********************************************************************************************************************** -void GetSeqsCommand::readList(){ +int GetSeqsCommand::readList(){ try { - if (outputDir == "") { outputDir += hasPath(listfile); } - string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" + getExtension(listfile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ifstream in; - openInputFile(listfile, in); + m->openInputFile(listfile, in); bool wroteSomething = false; while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + //read in list vector ListVector list(in); @@ -253,14 +348,17 @@ void GetSeqsCommand::readList(){ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length()); //if that name is in the .accnos file, add it - if (names.count(name) == 1) { newNames += name + ","; } + if (names.count(name) != 0) { newNames += name + ","; } } //get last name - if (names.count(binnames) == 1) { newNames += binnames; } + if (names.count(binnames) != 0) { newNames += binnames + ","; } //if there are names in this bin add to new list - if (newNames != "") { newList.push_back(newNames); } + if (newNames != "") { + newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma + newList.push_back(newNames); + } } //print new listvector @@ -269,41 +367,48 @@ void GetSeqsCommand::readList(){ newList.print(out); } - gobble(in); + m->gobble(in); } in.close(); out.close(); - if (wroteSomething == false) { - mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine(); - remove(outputFileName.c_str()); - } + 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); + + return 0; } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "readList"); + m->errorOut(e, "GetSeqsCommand", "readList"); exit(1); } } //********************************************************************************************************************** -void GetSeqsCommand::readName(){ +int GetSeqsCommand::readName(){ try { - if (outputDir == "") { outputDir += hasPath(namefile); } - string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); + ifstream in; - openInputFile(namefile, in); + m->openInputFile(namefile, in); string name, firstCol, secondCol; bool wroteSomething = false; while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } in >> firstCol; - in >> secondCol; + in >> secondCol; + + string hold = ""; + if (dups) { hold = secondCol; } vector parsedNames; //parse second column saving each name @@ -318,112 +423,165 @@ void GetSeqsCommand::readName(){ vector validSecond; for (int i = 0; i < parsedNames.size(); i++) { - if (names.count(parsedNames[i]) == 1) { + if (names.count(parsedNames[i]) != 0) { validSecond.push_back(parsedNames[i]); } } - - //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) == 1) { - + 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; - - 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) { + //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 << validSecond[0] << '\t'; - + 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; + } } } - - gobble(in); + m->gobble(in); } in.close(); out.close(); - if (wroteSomething == false) { - mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine(); - remove(outputFileName.c_str()); - } + 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); + + return 0; } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "readName"); + m->errorOut(e, "GetSeqsCommand", "readName"); exit(1); } } //********************************************************************************************************************** -void GetSeqsCommand::readGroup(){ +int GetSeqsCommand::readGroup(){ try { - if (outputDir == "") { outputDir += hasPath(groupfile); } - string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); + ifstream in; - openInputFile(groupfile, in); + m->openInputFile(groupfile, in); string name, group; bool wroteSomething = false; while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); 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) == 1) { + if (names.count(name) != 0) { wroteSomething = true; out << name << '\t' << group << endl; - - names.erase(name); } - gobble(in); + m->gobble(in); } in.close(); out.close(); - if (wroteSomething == false) { - mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine(); - remove(outputFileName.c_str()); - } + 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); + + return 0; } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "readGroup"); + 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; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); 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; + } + + 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); + + 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 -void GetSeqsCommand::readAlign(){ +int GetSeqsCommand::readAlign(){ try { - if (outputDir == "") { outputDir += hasPath(alignfile); } - string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report"; + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report"; ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); + ifstream in; - openInputFile(alignfile, in); + m->openInputFile(alignfile, in); string name, junk; bool wroteSomething = false; @@ -436,11 +594,14 @@ void GetSeqsCommand::readAlign(){ out << endl; while(!in.eof()){ + + if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + in >> name; //read from first column //if this name is in the accnos file - if (names.count(name) == 1) { + if (names.count(name) != 0) { wroteSomething = true; out << name << '\t'; @@ -452,8 +613,6 @@ void GetSeqsCommand::readAlign(){ } out << endl; - names.erase(name); - }else {//still read just don't do anything with it //read rest for (int i = 0; i < 15; i++) { @@ -462,29 +621,29 @@ void GetSeqsCommand::readAlign(){ } } - gobble(in); + m->gobble(in); } in.close(); out.close(); - if (wroteSomething == false) { - mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine(); - remove(outputFileName.c_str()); - } + 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); + + return 0; } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "readAlign"); + m->errorOut(e, "GetSeqsCommand", "readAlign"); exit(1); } } //********************************************************************************************************************** -void GetSeqsCommand::readAccnos(){ +int GetSeqsCommand::readAccnos(){ try { ifstream in; - openInputFile(accnosfile, in); + m->openInputFile(accnosfile, in); string name; while(!in.eof()){ @@ -492,13 +651,15 @@ void GetSeqsCommand::readAccnos(){ names.insert(name); - gobble(in); + m->gobble(in); } - in.close(); + in.close(); + + return 0; } catch(exception& e) { - errorOut(e, "GetSeqsCommand", "readAccnos"); + m->errorOut(e, "GetSeqsCommand", "readAccnos"); exit(1); } }