X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=2abe9ef78a8c76354d377087fa7a23deb27b4d25;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=1990e9c364d6bdedb257f2801abe55f566de8e29;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp index 1990e9c..2abe9ef 100644 --- a/removeseqscommand.cpp +++ b/removeseqscommand.cpp @@ -12,21 +12,54 @@ #include "listvector.hpp" //********************************************************************************************************************** -vector RemoveSeqsCommand::getValidParameters(){ +vector RemoveSeqsCommand::setParameters(){ try { - string Array[] = {"fasta","name", "group", "alignreport", "accnos", "qfile","list","taxonomy","outputdir","inputdir", "dups" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + 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); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "RemoveSeqsCommand", "getValidParameters"); + m->errorOut(e, "RemoveSeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string RemoveSeqsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n"; + helpString += "It outputs a file containing the sequences NOT in the .accnos file.\n"; + helpString += "The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos and at least one of the file parameters.\n"; + helpString += "The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n"; + helpString += "The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n"; + helpString += "Example remove.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, "RemoveSeqsCommand", "getHelpString"); exit(1); } } + + //********************************************************************************************************************** RemoveSeqsCommand::RemoveSeqsCommand(){ try { abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["taxonomy"] = tempOutNames; @@ -42,40 +75,16 @@ RemoveSeqsCommand::RemoveSeqsCommand(){ } } //********************************************************************************************************************** -vector RemoveSeqsCommand::getRequiredParameters(){ - try { - string Array[] = {"accnos"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RemoveSeqsCommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector RemoveSeqsCommand::getRequiredFiles(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RemoveSeqsCommand", "getRequiredFiles"); - exit(1); - } -} -//********************************************************************************************************************** RemoveSeqsCommand::RemoveSeqsCommand(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 { - //valid paramters for this command - string Array[] = {"fasta","name", "group", "alignreport", "accnos", "qfile", "list","taxonomy","outputdir","inputdir", "dups" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -175,19 +184,29 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { //check for required parameters accnosfile = validParameter.validFile(parameters, "accnos", true); if (accnosfile == "not open") { abort = true; } - else if (accnosfile == "not found") { accnosfile = ""; m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); 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); } fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = 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") { abort = 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 if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } @@ -196,15 +215,17 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { 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") { 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); } string usedDups = "true"; string temp = validParameter.validFile(parameters, "dups", false); @@ -216,7 +237,10 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; } - if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; } + if ((fastafile != "") && (namefile == "")) { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } } } @@ -227,24 +251,6 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { } //********************************************************************************************************************** -void RemoveSeqsCommand::help(){ - try { - m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n"); - m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n"); - m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos and at least one of the file parameters.\n"); - m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n"); - m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n"); - m->mothurOut("Example remove.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) { - m->errorOut(e, "RemoveSeqsCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - int RemoveSeqsCommand::execute(){ try { @@ -264,10 +270,8 @@ int RemoveSeqsCommand::execute(){ if (taxfile != "") { readTax(); } if (qualfile != "") { readQual(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - - m->mothurOut("Removed " + toString(names.size()) + " sequences."); m->mothurOutEndLine(); - + if (m->control_pressed) { 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(); @@ -331,9 +335,10 @@ int RemoveSeqsCommand::readFasta(){ string name; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } Sequence currSeq(in); name = currSeq.getName(); @@ -344,7 +349,7 @@ int RemoveSeqsCommand::readFasta(){ wroteSomething = true; currSeq.printSequence(out); - } + }else { removedCount++; } } m->gobble(in); } @@ -354,6 +359,8 @@ int RemoveSeqsCommand::readFasta(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine(); + return 0; } @@ -377,6 +384,7 @@ int RemoveSeqsCommand::readQual(){ string name; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ @@ -408,7 +416,7 @@ int RemoveSeqsCommand::readQual(){ wroteSomething = true; out << name << endl << scores; - } + }else { removedCount++; } m->gobble(in); } @@ -419,6 +427,8 @@ int RemoveSeqsCommand::readQual(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your quality file."); m->mothurOutEndLine(); + return 0; } @@ -441,8 +451,12 @@ int RemoveSeqsCommand::readList(){ m->openInputFile(listfile, in); bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ + + removedCount = 0; + //read in list vector ListVector list(in); @@ -452,7 +466,7 @@ int RemoveSeqsCommand::readList(){ //for each bin for (int i = 0; i < list.getNumBins(); i++) { - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } //parse out names that are in accnos file string binnames = list.get(i); @@ -464,10 +478,12 @@ int RemoveSeqsCommand::readList(){ //if that name is in the .accnos file, add it if (names.count(name) == 0) { newNames += name + ","; } + else { removedCount++; } } //get last name if (names.count(binnames) == 0) { newNames += binnames + ","; } + else { removedCount++; } //if there are names in this bin add to new list if (newNames != "") { @@ -489,7 +505,9 @@ int RemoveSeqsCommand::readList(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName); - + + m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine(); + return 0; } @@ -513,24 +531,17 @@ int RemoveSeqsCommand::readName(){ string name, firstCol, secondCol; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } - + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + in >> firstCol; m->gobble(in); in >> secondCol; - + vector parsedNames; - //parse second column saving each name - while (secondCol.find_first_of(',') != -1) { - name = secondCol.substr(0,secondCol.find_first_of(',')); - secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length()); - parsedNames.push_back(name); - } + m->splitAtComma(secondCol, parsedNames); - //get name after last , - parsedNames.push_back(secondCol); - vector validSecond; validSecond.clear(); for (int i = 0; i < parsedNames.size(); i++) { if (names.count(parsedNames[i]) == 0) { @@ -540,8 +551,10 @@ int RemoveSeqsCommand::readName(){ if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); } + removedCount += parsedNames.size(); }else { - //if the name in the first column is in the set then print it and any other names in second column also in set + removedCount += parsedNames.size()-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; @@ -572,10 +585,12 @@ int RemoveSeqsCommand::readName(){ } in.close(); out.close(); - + if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName); - + + m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine(); + return 0; } catch(exception& e) { @@ -599,9 +614,10 @@ int RemoveSeqsCommand::readGroup(){ string name, group; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + 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 @@ -610,7 +626,7 @@ int RemoveSeqsCommand::readGroup(){ if (names.count(name) == 0) { wroteSomething = true; out << name << '\t' << group << endl; - } + }else { removedCount++; } m->gobble(in); } @@ -620,6 +636,9 @@ int RemoveSeqsCommand::readGroup(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine(); + + return 0; } catch(exception& e) { @@ -641,9 +660,10 @@ int RemoveSeqsCommand::readTax(){ string name, tax; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + 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 @@ -652,7 +672,7 @@ int RemoveSeqsCommand::readTax(){ if (names.count(name) == 0) { wroteSomething = true; out << name << '\t' << tax << endl; - } + }else { removedCount++; } m->gobble(in); } @@ -662,6 +682,8 @@ int RemoveSeqsCommand::readTax(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine(); + return 0; } catch(exception& e) { @@ -685,6 +707,7 @@ int RemoveSeqsCommand::readAlign(){ string name, junk; bool wroteSomething = false; + int removedCount = 0; //read column headers for (int i = 0; i < 16; i++) { @@ -694,7 +717,7 @@ int RemoveSeqsCommand::readAlign(){ out << endl; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column @@ -712,6 +735,7 @@ int RemoveSeqsCommand::readAlign(){ out << endl; }else {//still read just don't do anything with it + removedCount++; //read rest for (int i = 0; i < 15; i++) { @@ -728,6 +752,9 @@ int RemoveSeqsCommand::readAlign(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["alignreport"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your alignreport file."); m->mothurOutEndLine(); + + return 0; }