From: Sarah Westcott Date: Mon, 6 Feb 2012 18:46:47 +0000 (-0500) Subject: added sort.seqs command. puts sequences from a fasta, name, group, quality or taxono... X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=88cf5f80fc06dbd9e95d14bcefc63aba8759d544 added sort.seqs command. puts sequences from a fasta, name, group, quality or taxonomy file in the same order. may provide a accnos file it you wish to specify order used. large parameter can be set to true if the fasta or qfile is too large to fit in memory. --- diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 545f7b3..978ff0b 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -53,6 +53,7 @@ A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A79234D613C74BF6002B08E2 /* mothurfisher.cpp */; }; A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A795840C13F13CD900F201D5 /* countgroupscommand.cpp */; }; A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; }; + A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */; }; A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */; }; A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; }; A7BF221414587886000AD524 /* myPerseus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7BF221214587886000AD524 /* myPerseus.cpp */; }; @@ -472,6 +473,8 @@ A795840C13F13CD900F201D5 /* countgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countgroupscommand.cpp; sourceTree = ""; }; A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = ""; }; A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = ""; }; + A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sortseqscommand.cpp; sourceTree = ""; }; + A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sortseqscommand.h; sourceTree = ""; }; A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuassociationcommand.cpp; sourceTree = ""; }; A7A3C8C814D041AD00B1BFBE /* otuassociationcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuassociationcommand.h; sourceTree = ""; }; A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = ""; }; @@ -1489,6 +1492,8 @@ A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, A774101214695AF60098E6AC /* shhhseqscommand.h */, A774101314695AF60098E6AC /* shhhseqscommand.cpp */, + A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */, + A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */, A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, @@ -2277,6 +2282,7 @@ A7FA2B1614A0EBEA007C09A6 /* sslvrg.f in Sources */, A7FA2B5B14A0F0C2007C09A6 /* intrv.f in Sources */, A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */, + A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; diff --git a/commandfactory.cpp b/commandfactory.cpp index d813e1b..75fad85 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -127,6 +127,7 @@ #include "shhhseqscommand.h" #include "summaryqualcommand.h" #include "otuassociationcommand.h" +#include "sortseqscommand.h" /*******************************************************/ @@ -275,6 +276,7 @@ CommandFactory::CommandFactory(){ commands["summary.qual"] = "summary.qual"; commands["shhh.seqs"] = "shhh.seqs"; commands["otu.association"] = "otu.association"; + commands["sort.seqs"] = "sort.seqs"; commands["quit"] = "MPIEnabled"; } @@ -436,6 +438,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); } else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(optionString); } else if(commandName == "otu.association") { command = new OTUAssociationCommand(optionString); } + else if(commandName == "sort.seqs") { command = new SortSeqsCommand(optionString); } else { command = new NoCommand(optionString); } return command; @@ -581,6 +584,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); } else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); } else if(commandName == "otu.association") { pipecommand = new OTUAssociationCommand(optionString); } + else if(commandName == "sort.seqs") { pipecommand = new SortSeqsCommand(optionString); } else { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -714,6 +718,7 @@ Command* CommandFactory::getCommand(string commandName){ else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); } else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); } else if(commandName == "otu.association") { shellcommand = new OTUAssociationCommand(); } + else if(commandName == "sort.seqs") { shellcommand = new SortSeqsCommand(); } else { shellcommand = new NoCommand(); } return shellcommand; diff --git a/sortseqscommand.cpp b/sortseqscommand.cpp new file mode 100644 index 0000000..1cc142f --- /dev/null +++ b/sortseqscommand.cpp @@ -0,0 +1,877 @@ +// +// sortseqscommand.cpp +// Mothur +// +// Created by Sarah Westcott on 2/3/12. +// Copyright (c) 2012 Schloss Lab. All rights reserved. +// + +#include "sortseqscommand.h" +#include "sequence.hpp" +#include "qualityscores.h" + +//********************************************************************************************************************** +vector SortSeqsCommand::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 ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile); + CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos); + 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, "SortSeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string SortSeqsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The sort.seqs command puts the sequences in the same order for the following file types: accnos fasta, name, group, taxonomy or quality file.\n"; + helpString += "The sort.seqs command parameters are accnos, fasta, name, group, taxonomy, qfile and large.\n"; + helpString += "The accnos file allows you to specify the order you want the files in. If none is provided, mothur will use the order of the first file it reads.\n"; + helpString += "The large parameters is used to indicate your files are too large to fit in RAM.\n"; + helpString += "The sort.seqs command should be in the following format: sort.seqs(fasta=yourFasta).\n"; + helpString += "Example sort.seqs(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, "SortSeqsCommand", "getHelpString"); + exit(1); + } +} + + +//********************************************************************************************************************** +SortSeqsCommand::SortSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +SortSeqsCommand::SortSeqsCommand(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["qfile"] = 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("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("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; } + } + + 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; } + } + } + + + //check for parameters + accnosfile = validParameter.validFile(parameters, "accnos", true); + if (accnosfile == "not open") { accnosfile = ""; abort = true; } + else if (accnosfile == "not found") { accnosfile = ""; } + else { m->setAccnosFile(accnosfile); } + + 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); } + + 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 temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "f"; } + large = m->isTrue(temp); + + if ((fastafile == "") && (namefile == "") && (groupfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy or quality."); m->mothurOutEndLine(); abort = true; } + + if ((fastafile != "") && (namefile == "")) { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } + + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int SortSeqsCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //read through the correct file and output lines you want to keep + if (accnosfile != "") { readAccnos(); } + if (fastafile != "") { readFasta(); } + if (qualfile != "") { readQual(); } + if (namefile != "") { readName(); } + if (groupfile != "") { readGroup(); } + if (taxfile != "") { readTax(); } + + 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(); + 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("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, "SortSeqsCommand", "execute"); + exit(1); + } +} + +//********************************************************************************************************************** +int SortSeqsCommand::readFasta(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "sorted" + m->getExtension(fastafile); + outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(fastafile, in); + string name; + + if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have + + if (large) { //if the file is too large to fit in memory we can still process it, but the io will be very time consuming. + //read through the file looking for 1000 seqs at a time. Once we find them output them and start looking for the next 1000. + //this way we only store 1000 seqs in memory at a time. + + int numNames = names.size(); + int numNamesInFile = 0; + + //to make sure we dont miss any seqs, add any seqs that are not in names but in the file to the end of names + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + Sequence currSeq(in); + name = currSeq.getName(); + + if (name != "") { + numNamesInFile++; + map::iterator it = names.find(name); + if (it == names.end()) { + names[name] = numNames; numNames++; + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + m->gobble(in); + } + in.close(); + out.close(); + + int numLeft = names.size(); + if (numNamesInFile < numLeft) { numLeft = numNamesInFile; } + + int size = 1000; //assume that user can hold 1000 seqs in memory + if (numLeft < size) { size = numLeft; } + int times = 0; + + vector seqs; seqs.resize(size); + + while (numLeft > 0) { + + ifstream in2; + m->openInputFile(fastafile, in2); + + if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; } + + int found = 0; + int needToFind = size; + if (numLeft < size) { needToFind = numLeft; } + + while(!in2.eof()){ + if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; } + + //stop reading if we already found the seqs we are looking for + if (found >= needToFind) { break; } + + Sequence currSeq(in2); + name = currSeq.getName(); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + //is it in the set of seqs we are looking for this time around + int thisSeqsPlace = it->second; + thisSeqsPlace -= (times * size); + if ((thisSeqsPlace < size) && (thisSeqsPlace >= 0)) { + seqs[thisSeqsPlace] = currSeq; + found++; + } + }else { m->mothurOut("[ERROR]: in logic of readFasta function.\n"); m->control_pressed = true; } + } + m->gobble(in2); + } + in2.close(); + + ofstream out2; + m->openOutputFileAppend(outputFileName, out2); + + int output = seqs.size(); + if (numLeft < seqs.size()) { output = numLeft; } + + for (int i = 0; i < output; i++) { + seqs[i].printSequence(out2); + } + out2.close(); + + times++; + numLeft -= output; + } + + m->mothurOut("Ordered " + toString(numNamesInFile) + " sequences from " + fastafile + ".\n"); + }else { + + vector seqs; seqs.resize(names.size()); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + Sequence currSeq(in); + name = currSeq.getName(); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + seqs[it->second] = currSeq; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back(currSeq); + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + m->gobble(in); + } + in.close(); + + for (int i = 0; i < seqs.size(); i++) { + seqs[i].printSequence(out); + } + out.close(); + + m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + fastafile + ".\n"); + } + + }else { //read in file to fill names + int count = 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 + names[name] = count; + count++; + currSeq.printSequence(out); + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + fastafile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readFasta"); + exit(1); + } +} +//********************************************************************************************************************** +int SortSeqsCommand::readQual(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "sorted" + m->getExtension(qualfile); + outputTypes["qfile"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(qualfile, in); + string name; + + if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have + + if (large) { //if the file is too large to fit in memory we can still process it, but the io will be very time consuming. + //read through the file looking for 1000 seqs at a time. Once we find them output them and start looking for the next 1000. + //this way we only store 1000 seqs in memory at a time. + + int numNames = names.size(); + int numNamesInFile = 0; + + //to make sure we dont miss any seqs, add any seqs that are not in names but in the file to the end of names + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + QualityScores currQual; + currQual = QualityScores(in); + name = currQual.getName(); + + if (name != "") { + numNamesInFile++; + map::iterator it = names.find(name); + if (it == names.end()) { + names[name] = numNames; numNames++; + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + m->gobble(in); + } + in.close(); + out.close(); + + int numLeft = names.size(); + if (numNamesInFile < numLeft) { numLeft = numNamesInFile; } + + int size = 1000; //assume that user can hold 1000 seqs in memory + if (numLeft < size) { size = numLeft; } + int times = 0; + + + vector seqs; seqs.resize(size); + + while (numLeft > 0) { + + ifstream in2; + m->openInputFile(qualfile, in2); + + if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; } + + int found = 0; + int needToFind = size; + if (numLeft < size) { needToFind = numLeft; } + + while(!in2.eof()){ + if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; } + + //stop reading if we already found the seqs we are looking for + if (found >= needToFind) { break; } + + QualityScores currQual; + currQual = QualityScores(in2); + name = currQual.getName(); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + //is it in the set of seqs we are looking for this time around + int thisSeqsPlace = it->second; + thisSeqsPlace -= (times * size); + if ((thisSeqsPlace < size) && (thisSeqsPlace >= 0)) { + seqs[thisSeqsPlace] = currQual; + found++; + } + }else { m->mothurOut("[ERROR]: in logic of readQual function.\n"); m->control_pressed = true; } + } + m->gobble(in2); + } + in2.close(); + + ofstream out2; + m->openOutputFileAppend(outputFileName, out2); + + int output = seqs.size(); + if (numLeft < seqs.size()) { output = numLeft; } + + for (int i = 0; i < output; i++) { + seqs[i].printQScores(out2); + } + out2.close(); + + times++; + numLeft -= output; + } + + m->mothurOut("Ordered " + toString(numNamesInFile) + " sequences from " + qualfile + ".\n"); + + }else { + + vector seqs; seqs.resize(names.size()); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + QualityScores currQual; + currQual = QualityScores(in); + name = currQual.getName(); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + seqs[it->second] = currQual; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back(currQual); + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + m->gobble(in); + } + in.close(); + + for (int i = 0; i < seqs.size(); i++) { + seqs[i].printQScores(out); + } + out.close(); + + m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + qualfile + ".\n"); + } + + }else { //read in file to fill names + int count = 0; + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + QualityScores currQual; + currQual = QualityScores(in); + + m->gobble(in); + + if (currQual.getName() != "") { + //if this name is in the accnos file + names[currQual.getName()] = count; + count++; + currQual.printQScores(out); + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + qualfile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readQual"); + exit(1); + } +} +//********************************************************************************************************************** +int SortSeqsCommand::readName(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "sorted" + m->getExtension(namefile); + outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(namefile, in); + string name, firstCol, secondCol; + + if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have + + vector seqs; seqs.resize(names.size()); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> firstCol; m->gobble(in); + in >> secondCol; m->gobble(in); + + if (firstCol != "") { + map::iterator it = names.find(firstCol); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + seqs[it->second] = firstCol + '\t' + secondCol; + }else { //if we cant find it then add it to the end + names[firstCol] = seqs.size(); + seqs.push_back((firstCol + '\t' + secondCol)); + m->mothurOut(firstCol + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + } + in.close(); + + for (int i = 0; i < seqs.size(); i++) { + out << seqs[i] << endl; + } + out.close(); + + m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + namefile + ".\n"); + + }else { //read in file to fill names + int count = 0; + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> firstCol; m->gobble(in); + in >> secondCol; m->gobble(in); + + if (firstCol != "") { + //if this name is in the accnos file + names[firstCol] = count; + count++; + out << firstCol << '\t' << secondCol << endl; + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + namefile + " to determine the order. It contains " + toString(count) + " representative sequences.\n"); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readName"); + exit(1); + } +} + +//********************************************************************************************************************** +int SortSeqsCommand::readGroup(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); + outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(groupfile, in); + string name, group; + + if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have + + vector seqs; seqs.resize(names.size()); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; m->gobble(in); + in >> group; m->gobble(in); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + seqs[it->second] = name + '\t' + group; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back((name + '\t' + group)); + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + } + in.close(); + + for (int i = 0; i < seqs.size(); i++) { + out << seqs[i] << endl; + } + out.close(); + + m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + groupfile + ".\n"); + + }else { //read in file to fill names + int count = 0; + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; m->gobble(in); + in >> group; m->gobble(in); + + if (name != "") { + //if this name is in the accnos file + names[name] = count; + count++; + out << name << '\t' << group << endl; + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + groupfile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readGroup"); + exit(1); + } +} +//********************************************************************************************************************** +int SortSeqsCommand::readTax(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile); + outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(taxfile, in); + string name, tax; + + if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have + + vector seqs; seqs.resize(names.size()); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; m->gobble(in); + in >> tax; m->gobble(in); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + seqs[it->second] = name + '\t' + tax; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back((name + '\t' + tax)); + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + } + in.close(); + + for (int i = 0; i < seqs.size(); i++) { + out << seqs[i] << endl; + } + out.close(); + + m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + taxfile + ".\n"); + + }else { //read in file to fill names + int count = 0; + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; m->gobble(in); + in >> tax; m->gobble(in); + + if (name != "") { + //if this name is in the accnos file + names[name] = count; + count++; + out << name << '\t' << tax << endl; + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + taxfile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readTax"); + exit(1); + } +} +//********************************************************************************************************************** +int SortSeqsCommand::readAccnos(){ + try { + + ifstream in; + m->openInputFile(accnosfile, in); + string name; + int count = 0; + + while(!in.eof()){ + + if (m->control_pressed) { break; } + + in >> name; m->gobble(in); + + if (name != "") { + names[name] = count; + count++; + } + } + in.close(); + + m->mothurOut("\nUsing " + accnosfile + " to determine the order. It contains " + toString(count) + " representative sequences.\n"); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readAccnos"); + exit(1); + } +} + +//********************************************************************************************************************** + + + + + diff --git a/sortseqscommand.h b/sortseqscommand.h new file mode 100644 index 0000000..b807855 --- /dev/null +++ b/sortseqscommand.h @@ -0,0 +1,53 @@ +#ifndef Mothur_sortseqscommand_h +#define Mothur_sortseqscommand_h + + +// +// sortseqscommand.h +// Mothur +// +// Created by Sarah Westcott on 2/3/12. +// Copyright (c) 2012 Schloss Lab. All rights reserved. +// + + + +#include "command.hpp" + +class SortSeqsCommand : public Command { + +public: + + SortSeqsCommand(string); + SortSeqsCommand(); + ~SortSeqsCommand(){} + + vector setParameters(); + string getCommandName() { return "sort.seqs"; } + string getCommandCategory() { return "Sequence Processing"; } + string getHelpString(); + string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; } + string getDescription() { return "puts sequences from a fasta, name, group, quality or taxonomy file in the same order"; } + + int execute(); + void help() { m->mothurOut(getHelpString()); } + + +private: + map names; + string accnosfile, fastafile, namefile, groupfile, taxfile, qualfile, outputDir; + bool abort, large; + vector outputNames; + + int readFasta(); + int readName(); + int readGroup(); + int readAccnos(); + int readTax(); + int readQual(); + +}; + +#endif + +