*/
#include "chimeraslayercommand.h"
-#include "chimeraslayer.h"
#include "deconvolutecommand.h"
+#include "referencedb.h"
+#include "sequenceparser.h"
+#include "counttable.h"
//**********************************************************************************************************************
-vector<string> ChimeraSlayerCommand::getValidParameters(){
+vector<string> ChimeraSlayerCommand::setParameters(){
try {
- string AlignArray[] = {"fasta", "processors","trim", "name","window", "include","template","numwanted", "ksize", "match","mismatch",
- "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pwindow("window", "Number", "", "50", "", "", "","",false,false); parameters.push_back(pwindow);
+ CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pmatch("match", "Number", "", "5.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pminsim("minsim", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pminsim);
+ CommandParameter pmincov("mincov", "Number", "", "70", "", "", "","",false,false); parameters.push_back(pmincov);
+ CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pminsnp);
+ CommandParameter pminbs("minbs", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pminbs);
+ CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "","",false,false); parameters.push_back(psearch);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+
+ CommandParameter prealign("realign", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(prealign);
+ CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "","fasta",false,false); parameters.push_back(ptrim);
+ CommandParameter psplit("split", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psplit);
+ CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "","",false,false); parameters.push_back(pnumwanted);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "","",false,false); parameters.push_back(pdivergence);
+ CommandParameter pdups("dereplicate", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdups);
+ CommandParameter pparents("parents", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pparents);
+ CommandParameter pincrement("increment", "Number", "", "5", "", "", "","",false,false); parameters.push_back(pincrement);
+ CommandParameter pblastlocation("blastlocation", "String", "", "", "", "", "","",false,false); parameters.push_back(pblastlocation);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "getValidParameters");
+ m->errorOut(e, "ChimeraSlayerCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ChimeraSlayerCommand::ChimeraSlayerCommand(){
+string ChimeraSlayerCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["chimera"] = tempOutNames;
- outputTypes["accnos"] = tempOutNames;
- outputTypes["fasta"] = tempOutNames;
+ string helpString = "";
+ helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
+ helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
+ helpString += "The chimera.slayer command parameters are fasta, name, group, template, processors, dereplicate, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, blastlocation and realign.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
+ helpString += "The name parameter allows you to provide a name file, if you are using reference=self. \n";
+ helpString += "The group parameter allows you to provide a group file. The group file can be used with a namesfile and reference=self. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
+ helpString += "The count parameter allows you to provide a count file. The count file reference=self. If your count file contains group information, when checking sequences, only sequences from the same group as the query sequence will be used as the reference. When you use a count file with group info and dereplicate=T, mothur will create a *.pick.count_table file containing seqeunces after chimeras are removed. \n";
+ helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
+ helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+#ifdef USE_MPI
+ helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
+#endif
+ helpString += "If the dereplicate parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric, default=f.\n";
+ helpString += "The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n";
+ helpString += "The split parameter allows you to check both pieces of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n";
+ helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=50. \n";
+ helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n";
+ helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n";
+ helpString += "The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n";
+ helpString += "The match parameter allows you to reward matched bases in blast search, default is 5. \n";
+ helpString += "The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n";
+ helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
+ helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
+ helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n";
+ helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
+ helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
+ helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
+ helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n";
+ helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
+ helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true. \n";
+ helpString += "The blastlocation parameter allows you to specify the location of your blast executable. By default mothur will look in ./blast/bin relative to mothur's executable. \n";
+ helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
+ helpString += "The chimera.slayer command should be in the following format: \n";
+ helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
+ helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
+ m->errorOut(e, "ChimeraSlayerCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ChimeraSlayerCommand::getRequiredParameters(){
- try {
- string AlignArray[] = {"template","fasta"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "getRequiredParameters");
- exit(1);
- }
+string ChimeraSlayerCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "chimera") { pattern = "[filename],slayer.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],slayer.accnos"; }
+ else if (type == "fasta") { pattern = "[filename],slayer.fasta"; }
+ else if (type == "count") { pattern = "[filename],slayer.pick.count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> ChimeraSlayerCommand::getRequiredFiles(){
+ChimeraSlayerCommand::ChimeraSlayerCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "getRequiredFiles");
+ m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
exit(1);
}
}
ChimeraSlayerCommand::ChimeraSlayerCommand(string option) {
try {
abort = false; calledHelp = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
+ hasCount = false;
+ hasName = 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", "processors","name", "include","trim", "window", "template","numwanted", "ksize", "match","mismatch",
- "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//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);
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", false);
- if (fastafile == "not found") { fastafile = ""; m->mothurOut("[ERROR]: fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
- else {
+ if (fastafile == "not found") {
+ //if there is a current fasta file, use it
+ string filename = m->getFastaFile();
+ if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else {
m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
- if (inputDir != "") {
- string path = m->hasPath(fastaFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
- }
-
- int ableToOpen;
- ifstream in;
- ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+ bool ignore = false;
+ if (fastaFileNames[i] == "current") {
+ fastaFileNames[i] = m->getFastaFile();
+ if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
}
}
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
- }
-
- in.close();
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
+ }
}
}
//check for required parameters
- bool hasName = true;
namefile = validParameter.validFile(parameters, "name", false);
- if (namefile == "not found") { namefile = ""; hasName = false; }
+ if (namefile == "not found") { namefile = ""; }
else {
m->splitAtDash(namefile, nameFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < nameFileNames.size(); i++) {
- if (inputDir != "") {
- string path = m->hasPath(nameFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; }
- }
- int ableToOpen;
- ifstream in;
+ bool ignore = false;
+ if (nameFileNames[i] == "current") {
+ nameFileNames[i] = m->getNameFile();
+ if (nameFileNames[i] != "") { m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ nameFileNames.erase(nameFileNames.begin()+i);
+ i--;
+ }
+ }
- ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(nameFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
+ m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ nameFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
+ m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ nameFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ nameFileNames.erase(nameFileNames.begin()+i);
+ i--;
+ }else {
+ m->setNameFile(nameFileNames[i]);
+ }
+ }
+ }
+ }
+
+ if (nameFileNames.size() != 0) { hasName = true; }
+
+ //check for required parameters
+ vector<string> countfileNames;
+ countfile = validParameter.validFile(parameters, "count", false);
+ if (countfile == "not found") {
+ countfile = "";
+ }else {
+ m->splitAtDash(countfile, countfileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < countfileNames.size(); i++) {
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
- m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- nameFileNames[i] = tryPath;
+ bool ignore = false;
+ if (countfileNames[i] == "current") {
+ countfileNames[i] = m->getCountTableFile();
+ if (nameFileNames[i] != "") { m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ countfileNames.erase(countfileNames.begin()+i);
+ i--;
}
}
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
- m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- nameFileNames[i] = tryPath;
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(countfileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { countfileNames[i] = inputDir + countfileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(countfileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]);
+ m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ countfileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
+ m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ countfileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ countfileNames.erase(countfileNames.begin()+i);
+ i--;
+ }else {
+ m->setCountTableFile(countfileNames[i]);
}
}
+ }
+ }
+
+ if (countfileNames.size() != 0) { hasCount = true; }
+
+ //make sure there is at least one valid file left
+ if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
+ if (!hasName && hasCount) { nameFileNames = countfileNames; }
+
+ if ((hasCount || hasName) && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of name or count files does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
+
+ bool hasGroup = true;
+ groupfile = validParameter.validFile(parameters, "group", false);
+ if (groupfile == "not found") { groupfile = ""; hasGroup = false; }
+ else {
+ m->splitAtDash(groupfile, groupFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < groupFileNames.size(); i++) {
- in.close();
+ bool ignore = false;
+ if (groupFileNames[i] == "current") {
+ groupFileNames[i] = m->getGroupFile();
+ if (groupFileNames[i] != "") { m->mothurOut("Using " + groupFileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ groupFileNames.erase(groupFileNames.begin()+i);
+ i--;
+ }
+ }
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- nameFileNames.erase(nameFileNames.begin()+i);
- i--;
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(groupFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { groupFileNames[i] = inputDir + groupFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(groupFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(groupFileNames[i]);
+ m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(groupFileNames[i]);
+ m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + groupFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ groupFileNames.erase(groupFileNames.begin()+i);
+ i--;
+ }else {
+ m->setGroupFile(groupFileNames[i]);
+ }
}
}
//make sure there is at least one valid file left
- if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
+ if (groupFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid group files."); m->mothurOutEndLine(); abort = true; }
}
- if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
+ if (hasGroup && (groupFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of groupfiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
+ if (hasGroup && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
//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 = ""; }
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ rdb->save = save;
+ if (save) { //clear out old references
+ rdb->clearMemory();
+ }
string path;
- it = parameters.find("template");
+ it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
- if (it->second == "self") { templatefile = "self"; }
+ if (it->second == "self") {
+ templatefile = "self";
+ if (save) {
+ m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
+ m->mothurOutEndLine();
+ save = false;
+ }
+ }
else {
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["template"] = inputDir + it->second; }
+ if (path == "") { parameters["reference"] = inputDir + it->second; }
- templatefile = validParameter.validFile(parameters, "template", true);
+ templatefile = validParameter.validFile(parameters, "reference", true);
if (templatefile == "not open") { abort = true; }
- else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
+ else if (templatefile == "not found") { //check for saved reference sequences
+ if (rdb->referenceSeqs.size() != 0) {
+ templatefile = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { if (save) { rdb->setSavedReference(templatefile); } }
}
+ }else if (hasName) { templatefile = "self";
+ if (save) {
+ m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
+ m->mothurOutEndLine();
+ save = false;
+ }
+ }else if (hasCount) { templatefile = "self";
+ if (save) {
+ m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
+ m->mothurOutEndLine();
+ save = false;
+ }
+ }
+ else {
+ if (rdb->referenceSeqs.size() != 0) {
+ templatefile = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ m->mothurOutEndLine();
+ templatefile = ""; abort = true;
+ }
}
- string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
- convert(temp, processors);
- includeAbunds = validParameter.validFile(parameters, "include", false); if (includeAbunds == "not found") { includeAbunds = "greater"; }
- if ((includeAbunds != "greater") && (includeAbunds != "greaterequal") && (includeAbunds != "all")) { includeAbunds = "greater"; m->mothurOut("Invalid include setting. options are greater, greaterequal or all. using greater."); m->mothurOutEndLine(); }
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
- convert(temp, ksize);
+ m->mothurConvert(temp, ksize);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; }
- convert(temp, window);
+ m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; }
- convert(temp, match);
+ m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
- convert(temp, mismatch);
+ m->mothurConvert(temp, mismatch);
temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
- convert(temp, divR);
+ m->mothurConvert(temp, divR);
temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
- convert(temp, minSimilarity);
+ m->mothurConvert(temp, minSimilarity);
temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
- convert(temp, minCoverage);
+ m->mothurConvert(temp, minCoverage);
temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
- convert(temp, minBS);
+ m->mothurConvert(temp, minBS);
- temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "100"; }
- convert(temp, minSNP);
+ temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
+ m->mothurConvert(temp, minSNP);
temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
- convert(temp, parents);
+ m->mothurConvert(temp, parents);
- temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; }
+ temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; }
realign = m->isTrue(temp);
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
trim = m->isTrue(temp);
- //temp = validParameter.validFile(parameters, "trimera", false); if (temp == "not found") { temp = "f"; }
- //trimera = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; }
+ trimera = m->isTrue(temp);
- search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
+ search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "blast"; }
- temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
- convert(temp, iters);
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
- convert(temp, increment);
+ m->mothurConvert(temp, increment);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
- convert(temp, numwanted);
+ m->mothurConvert(temp, numwanted);
+
+ temp = validParameter.validFile(parameters, "dereplicate", false);
+ if (temp == "not found") { temp = "false"; }
+ dups = m->isTrue(temp);
+
+ blastlocation = validParameter.validFile(parameters, "blastlocation", false);
+ if (blastlocation == "not found") { blastlocation = ""; }
+ else {
+ //add / to name if needed
+ string lastChar = blastlocation.substr(blastlocation.length()-1);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if (lastChar != "/") { blastlocation += "/"; }
+#else
+ if (lastChar != "\\") { blastlocation += "\\"; }
+#endif
+ blastlocation = m->getFullPathName(blastlocation);
+ string formatdbCommand = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = blastlocation + "formatdb";
+#else
+ formatdbCommand = blastlocation + "formatdb.exe";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in;
+ formatdbCommand = m->getFullPathName(formatdbCommand);
+ int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
+
+ string blastCommand = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = blastlocation + "megablast";
+#else
+ blastCommand = blastlocation + "megablast.exe";
+#endif
+ //test to make sure formatdb exists
+ ifstream in2;
+ blastCommand = m->getFullPathName(blastCommand);
+ ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
+
+ if ((hasName || hasCount) && (templatefile != "self")) { m->mothurOut("You have provided a namefile or countfile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+ if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
- if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
+ //until we resolve the issue 10-18-11
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+ //processors=1;
+#endif
}
}
catch(exception& e) {
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ChimeraSlayerCommand::help(){
- try {
-
- m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
- m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
- m->mothurOut("The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
- m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
- m->mothurOut("The name parameter allows you to provide a name file, if you are using template=self. \n");
- m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n");
- m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n");
- m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
- #ifdef USE_MPI
- m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
- #endif
- m->mothurOut("The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n");
- //m->mothurOut("The trimera parameter allows you to check both peices of a chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n");
- m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
- m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
- m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
- m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n");
- m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n");
- m->mothurOut("The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n");
- m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n");
- m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n");
- m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n");
- m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
- m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
- m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
- m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n");
- m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
- m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n");
- m->mothurOut("The chimera.slayer command should be in the following format: \n");
- m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
- m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-ChimeraSlayerCommand::~ChimeraSlayerCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int ChimeraSlayerCommand::execute(){
try{
-
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+
for (int s = 0; s < fastaFileNames.size(); s++) {
m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
int start = time(NULL);
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string outputFileName = getOutputFileName("chimera", variables);
+ string accnosFileName = getOutputFileName("accnos", variables);
+ string trimFastaFileName = getOutputFileName("fasta", variables);
+ string newCountFile = "";
- if (templatefile != "self") { //you want to run slayer with a refernce template
- chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
- }else {
- if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
- chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFileNames[s], search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
- }else {
-
- m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
-
- //use unique.seqs to create new name and fastafile
- string inputString = "fasta=" + fastaFileNames[s];
- m->mothurOut("/******************************************/"); m->mothurOutEndLine();
- m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
-
- Command* uniqueCommand = new DeconvoluteCommand(inputString);
- uniqueCommand->execute();
-
- map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
-
- delete uniqueCommand;
-
- m->mothurOut("/******************************************/"); m->mothurOutEndLine();
-
- string nameFile = filenames["name"][0];
- fastaFileNames[s] = filenames["fasta"][0];
-
- chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFile, search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
- }
- }
-
- if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.accnos";
- string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.fasta";
-
- if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
-
- if (chimera->getUnaligned()) {
- m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
- delete chimera;
- return 0;
- }
- templateSeqsLength = chimera->getLength();
+ //clears files
+ ofstream out, out1, out2;
+ m->openOutputFile(outputFileName, out); out.close();
+ m->openOutputFile(accnosFileName, out1); out1.close();
+ if (trim) { m->openOutputFile(trimFastaFileName, out2); out2.close(); }
+ outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
+ outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
+ if (trim) { outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
- #ifdef USE_MPI
- int pid, numSeqsPerProcessor;
- int tag = 2001;
- vector<unsigned long int> MPIPos;
-
- MPI_Status status;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- MPI_File inMPI;
- MPI_File outMPI;
- MPI_File outMPIAccnos;
- MPI_File outMPIFasta;
-
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- int inMode=MPI_MODE_RDONLY;
-
- char outFilename[1024];
- strcpy(outFilename, outputFileName.c_str());
-
- char outAccnosFilename[1024];
- strcpy(outAccnosFilename, accnosFileName.c_str());
+ //maps a filename to priority map.
+ //if no groupfile this is fastafileNames[s] -> prioirity
+ //if groupfile then this is each groups seqs -> priority
+ map<string, map<string, int> > fileToPriority;
+ map<string, map<string, int> >::iterator itFile;
+ map<string, string> fileGroup;
+ fileToPriority[fastaFileNames[s]] = priority; //default
+ fileGroup[fastaFileNames[s]] = "noGroup";
+ map<string, string> uniqueNames;
+ int totalChimeras = 0;
+ lines.clear();
- char outFastaFilename[1024];
- strcpy(outFastaFilename, trimFastaFileName.c_str());
-
- char inFileName[1024];
- strcpy(inFileName, fastaFileNames[s].c_str());
-
- MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
- MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
- MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
- if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
-
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (templatefile == "self") {
+ if (hasCount) {
+ SequenceCountParser* parser = NULL;
+ setUpForSelfReference(parser, fileGroup, fileToPriority, s);
+ if (parser != NULL) { uniqueNames = parser->getAllSeqsMap(); delete parser; }
+ }else {
+ SequenceParser* parser = NULL;
+ setUpForSelfReference(parser, fileGroup, fileToPriority, s);
+ if (parser != NULL) { uniqueNames = parser->getAllSeqsMap(); delete parser; }
+ }
+ }
- if (pid == 0) { //you are the root process
- m->mothurOutEndLine();
- m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
- m->mothurOutEndLine();
-
- string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
-
- //print header
- int length = outTemp.length();
- char* buf2 = new char[length];
- memcpy(buf2, outTemp.c_str(), length);
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
- MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
-
- MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
+ if (fileToPriority.size() == 1) { //you running without a groupfile
+ itFile = fileToPriority.begin();
+ string thisFastaName = itFile->first;
+ map<string, int> thisPriority = itFile->second;
+#ifdef USE_MPI
+ MPIExecute(thisFastaName, outputFileName, accnosFileName, trimFastaFileName, thisPriority);
+#else
+ //break up file
+ vector<unsigned long long> positions;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(thisFastaName, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ if (processors == 1) { lines.push_back(linePair(0, 1000)); }
+ else {
+ positions = m->setFilePosFasta(thisFastaName, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
- //send file positions to all processes
- for(int i = 1; i < processors; i++) {
- MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
}
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
-
- //do your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
-
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; }
-
- }else{ //you are a child process
- MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPIPos.resize(numSeqs+1);
- MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
-
- //do your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
-
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
}
+#endif
+ if(processors == 1){ numSeqs = driver(lines[0], outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority); }
+ else{ numSeqs = createProcesses(outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority); }
- //close files
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPI);
- MPI_File_close(&outMPIAccnos);
- if (trim) { MPI_File_close(&outMPIFasta); }
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-
- #else
- ofstream outHeader;
- string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
- m->openOutputFile(tempHeader, outHeader);
-
- chimera->printHeader(outHeader);
- outHeader.close();
-
- vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
-
- for (int i = 0; i < (positions.size()-1); i++) {
- lines.push_back(new linePair(positions[i], positions[(i+1)]));
- }
+ if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+#endif
+ }else { //you have provided a groupfile
+ string countFile = "";
+ if (hasCount) {
+ countFile = nameFileNames[s];
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFileNames[s]));
+ newCountFile = getOutputFileName("count", variables);
+ }
+#ifdef USE_MPI
+ MPIExecuteGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile, countFile);
+#else
+ if (processors == 1) {
+ numSeqs = driverGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile);
+ if (hasCount && dups) {
+ CountTable c; c.readTable(nameFileNames[s], true);
+ if (!m->isBlank(newCountFile)) {
+ ifstream in2;
+ m->openInputFile(newCountFile, in2);
+
+ string name, group;
+ while (!in2.eof()) {
+ in2 >> name >> group; m->gobble(in2);
+ c.setAbund(name, group, 0);
+ }
+ in2.close();
+ }
+ m->mothurRemove(newCountFile);
+ c.printTable(newCountFile);
+ }
- //break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
-
- if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
-
- }else{
- processIDS.resize(0);
-
- numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
-
- rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
- rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
- if (trim) { rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
-
- //append output files
- for(int i=1;i<processors;i++){
- m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
- remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
- }
-
- //append output files
- for(int i=1;i<processors;i++){
- m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
- remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
- }
-
- if (trim) {
- for(int i=1;i<processors;i++){
- m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
- remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str());
- }
- }
-
- if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
- }
+ }
+ else { numSeqs = createProcessesGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile, countFile); } //destroys fileToPriority
+#endif
- #else
- numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
-
- if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- #endif
+ if (pid == 0) {
+#endif
+ if (!dups) {
+ totalChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName, trimFastaFileName);
+ m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine();
+ }else {
+ if (hasCount) {
+ set<string> doNotRemove;
+ CountTable c; c.readTable(newCountFile, true);
+ vector<string> namesInTable = c.getNamesOfSeqs();
+ for (int i = 0; i < namesInTable.size(); i++) {
+ int temp = c.getNumSeqs(namesInTable[i]);
+ if (temp == 0) { c.remove(namesInTable[i]); }
+ else { doNotRemove.insert((namesInTable[i])); }
+ }
+ //remove names we want to keep from accnos file.
+ set<string> accnosNames = m->readAccnos(accnosFileName);
+ ofstream out2;
+ m->openOutputFile(accnosFileName, out2);
+ for (set<string>::iterator it = accnosNames.begin(); it != accnosNames.end(); it++) {
+ if (doNotRemove.count(*it) == 0) { out2 << (*it) << endl; }
+ }
+ out2.close();
+ c.printTable(newCountFile);
+ outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
+ }
+ }
+
+#ifdef USE_MPI
+ }
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
+#endif
+ }
- m->appendFiles(outputFileName, tempHeader);
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+ }
- remove(outputFileName.c_str());
- rename(tempHeader.c_str(), outputFileName.c_str());
-
- #endif
- delete chimera;
-
-
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
-
- outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
- outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
- if (trim) { outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
-
- m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+ //set accnos file as new current accnosfile
+ string current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
+ if (trim) {
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
}
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
}
}
//**********************************************************************************************************************
-
-int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){
+int ChimeraSlayerCommand::MPIExecuteGroups(string outputFileName, string accnosFileName, string trimFastaFileName, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist, string countfile){
try {
- ofstream out;
- m->openOutputFile(outputFName, out);
+#ifdef USE_MPI
+ int pid;
+ int tag = 2001;
- ofstream out2;
- m->openOutputFile(accnos, out2);
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ //put filenames in a vector, then pass each process a starting and ending point in the vector
+ //all processes already have the fileToPriority and fileGroup, they just need to know which files to process
+ map<string, map<string, int> >::iterator itFile;
+ vector<string> filenames;
+ for(itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) { filenames.push_back(itFile->first); }
- ofstream out3;
- if (trim) { m->openOutputFile(fasta, out3); }
+ int numGroupsPerProcessor = filenames.size() / processors;
+ int startIndex = pid * numGroupsPerProcessor;
+ int endIndex = (pid+1) * numGroupsPerProcessor;
+ if(pid == (processors - 1)){ endIndex = filenames.size(); }
- ifstream inFASTA;
- m->openInputFile(filename, inFASTA);
-
- inFASTA.seekg(filePos->start);
-
- bool done = false;
- int count = 0;
-
- while (!done) {
+ vector<unsigned long long> MPIPos;
- if (m->control_pressed) { out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1; }
+ MPI_File outMPI;
+ MPI_File outMPIAccnos;
+ MPI_File outMPIFasta;
+ MPI_File outMPICount;
- Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
-
- if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
-
- if (candidateSeq->getAligned().length() != templateSeqsLength) {
- m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
- }else{
- //find chimeras
- chimera->getChimeras(candidateSeq);
-
- if (m->control_pressed) { delete candidateSeq; return 1; }
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
- //print results
- Sequence* trimmed = chimera->print(out, out2);
-
- if (trim) { trimmed->printSequence(out3); delete trimmed; }
-
- //do you want to check both pieces for chimeras
- //if (trimera) {}
- }
- count++;
- }
- delete candidateSeq;
+ char outFilename[1024];
+ strcpy(outFilename, outputFileName.c_str());
+
+ char outAccnosFilename[1024];
+ strcpy(outAccnosFilename, accnosFileName.c_str());
+
+ char outFastaFilename[1024];
+ strcpy(outFastaFilename, trimFastaFileName.c_str());
+
+ char outCountFilename[1024];
+ strcpy(outCountFilename, countlist.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
+ MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
+ if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
+ if (hasCount && dups) { MPI_File_open(MPI_COMM_WORLD, outCountFilename, outMode, MPI_INFO_NULL, &outMPICount); }
+
+ if (m->control_pressed) { MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); if (hasCount && dups) { MPI_File_close(&outMPICount); } return 0; }
+
+ //print headers
+ if (pid == 0) { //you are the root process
+ m->mothurOutEndLine();
+ m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
+ m->mothurOutEndLine();
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- unsigned long int pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
- #else
- if (inFASTA.eof()) { break; }
- #endif
+ string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
- //report progress
- if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ //print header
+ int length = outTemp.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outTemp.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
+ delete buf2;
}
- //report progress
- if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
- out.close();
+ for (int i = startIndex; i < endIndex; i++) {
+
+ int start = time(NULL);
+ int num = 0;
+ string thisFastaName = filenames[i];
+ map<string, int> thisPriority = fileToPriority[thisFastaName];
+
+ char inFileName[1024];
+ strcpy(inFileName, thisFastaName.c_str());
+ MPI_File inMPI;
+ MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ MPIPos = m->setFilePosFasta(thisFastaName, num); //fills MPIPos, returns numSeqs
+
+ cout << endl << "Checking sequences from group: " << fileGroup[thisFastaName] << "." << endl;
+
+ set<string> cnames;
+ driverMPI(0, num, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, thisFastaName, thisPriority, true);
+ numSeqs += num;
+
+ MPI_File_close(&inMPI);
+ m->mothurRemove(thisFastaName);
+
+ if (dups) {
+ if (cnames.size() != 0) {
+ if (hasCount) {
+ for (set<string>::iterator it = cnames.begin(); it != cnames.end(); it++) {
+ string outputString = (*it) + "\t" + fileGroup[thisFastaName] + "\n";
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+ MPI_File_write_shared(outMPICount, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+ }
+ }else {
+ map<string, map<string, string> >::iterator itGroupNameMap = group2NameMap.find(fileGroup[thisFastaName]);
+ if (itGroupNameMap != group2NameMap.end()) {
+ map<string, string> thisnamemap = itGroupNameMap->second;
+ map<string, string>::iterator itN;
+ for (set<string>::iterator it = cnames.begin(); it != cnames.end(); it++) {
+ itN = thisnamemap.find(*it);
+ if (itN != thisnamemap.end()) {
+ vector<string> tempNames; m->splitAtComma(itN->second, tempNames);
+ for (int j = 0; j < tempNames.size(); j++) { //write to accnos file
+ string outputString = tempNames[j] + "\n";
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+
+ MPI_File_write_shared(outMPIAccnos, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+ }
+
+ }else { m->mothurOut("[ERROR]: parsing cannot find " + *it + ".\n"); m->control_pressed = true; }
+ }
+ }else { m->mothurOut("[ERROR]: parsing cannot find " + fileGroup[thisFastaName] + ".\n"); m->control_pressed = true; }
+ }
+
+ }
+ }
+
+ cout << endl << "It took " << toString(time(NULL) - start) << " secs to check " + toString(num) + " sequences from group " << fileGroup[thisFastaName] << "." << endl;
+ }
+
+ if (pid == 0) {
+ for(int i = 1; i < processors; i++) {
+ int temp = 0;
+ MPI_Recv(&temp, 1, MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
+ numSeqs += temp;
+ }
+ }else{ MPI_Send(&numSeqs, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD); }
+
+ MPI_File_close(&outMPI);
+ MPI_File_close(&outMPIAccnos);
+ if (trim) { MPI_File_close(&outMPIFasta); }
+ if (hasCount && dups) { MPI_File_close(&outMPICount); }
+
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
+#endif
+ return 0;
+
+ }catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "MPIExecuteGroups");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ChimeraSlayerCommand::MPIExecute(string inputFile, string outputFileName, string accnosFileName, string trimFastaFileName, map<string, int>& priority){
+ try {
+
+#ifdef USE_MPI
+ int pid, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<unsigned long long> MPIPos;
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ MPI_File inMPI;
+ MPI_File outMPI;
+ MPI_File outMPIAccnos;
+ MPI_File outMPIFasta;
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
+
+ char outFilename[1024];
+ strcpy(outFilename, outputFileName.c_str());
+
+ char outAccnosFilename[1024];
+ strcpy(outAccnosFilename, accnosFileName.c_str());
+
+ char outFastaFilename[1024];
+ strcpy(outFastaFilename, trimFastaFileName.c_str());
+
+ char inFileName[1024];
+ strcpy(inFileName, inputFile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
+ MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
+ if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); return 0; }
+
+ if (pid == 0) { //you are the root process
+ m->mothurOutEndLine();
+ m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
+ m->mothurOutEndLine();
+
+ string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
+
+ //print header
+ int length = outTemp.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outTemp.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+
+ MPIPos = m->setFilePosFasta(inputFile, numSeqs); //fills MPIPos, returns numSeqs
+
+ if (templatefile != "self") { //if template=self we can only use 1 processor
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+ }
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
+ if (templatefile == "self") { //if template=self we can only use 1 processor
+ startIndex = 0;
+ numSeqsPerProcessor = numSeqs;
+ }
+
+ //do your part
+ set<string> cnames;
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, inputFile, priority, false);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); return 0; }
+
+ }else{ //you are a child process
+ if (templatefile != "self") { //if template=self we can only use 1 processor
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(numSeqs+1);
+ MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
+ //do your part
+ set<string> cnames;
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, inputFile, priority, false);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); return 0; }
+
+ }
+ }
+
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPI);
+ MPI_File_close(&outMPIAccnos);
+ if (trim) { MPI_File_close(&outMPIFasta); }
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+
+#endif
+ return numSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "MPIExecute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ChimeraSlayerCommand::deconvoluteResults(map<string, string>& uniqueNames, string outputFileName, string accnosFileName, string trimFileName){
+ try {
+ map<string, string>::iterator itUnique;
+ int total = 0;
+
+ if (trimera) { //add in more potential uniqueNames
+ map<string, string> newUniqueNames = uniqueNames;
+ for (map<string, string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) {
+ newUniqueNames[(it->first)+"_LEFT"] = (it->first)+"_LEFT";
+ newUniqueNames[(it->first)+"_RIGHT"] = (it->first)+"_RIGHT";
+ }
+ uniqueNames = newUniqueNames;
+ newUniqueNames.clear();
+ }
+
+ //edit accnos file
+ ifstream in2;
+ m->openInputFile(accnosFileName, in2, "no error");
+
+ ofstream out2;
+ m->openOutputFile(accnosFileName+".temp", out2);
+
+ string name; name = "";
+ set<string> chimerasInFile;
+ set<string>::iterator itChimeras;
+
+ while (!in2.eof()) {
+ if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+
+ in2 >> name; m->gobble(in2);
+
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ itChimeras = chimerasInFile.find((itUnique->second));
+
+ if (itChimeras == chimerasInFile.end()) {
+ out2 << itUnique->second << endl;
+ chimerasInFile.insert((itUnique->second));
+ total++;
+ }
+ }
+ }
+ in2.close();
+ out2.close();
+
+ m->mothurRemove(accnosFileName);
+ rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
+
+
+ //edit chimera file
+ ifstream in;
+ m->openInputFile(outputFileName, in);
+
+ ofstream out;
+ m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ string rest, parent1, parent2, line;
+ set<string> namesInFile; //this is so if a sequence is found to be chimera in several samples we dont write it to the results file more than once
+ set<string>::iterator itNames;
+
+ //assumptions - in file each read will always look like...
+ /*
+ F11Fcsw_92754 no
+ F11Fcsw_63104 F11Fcsw_33372 F11Fcsw_37007 0.89441 80.4469 0.2 1.03727 93.2961 52.2 no 0-241 243-369
+ */
+
+ //get header line
+ if (!in.eof()) {
+ line = m->getline(in); m->gobble(in);
+ out << line << endl;
+ }
+
+ //for the chimera file, we want to make sure if any group finds a sequence to be chimeric then all groups do,
+ //so if this is a report that did not find it to be chimeric, but it appears in the accnos file,
+ //then ignore this report and continue until we find the report that found it to be chimeric
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; }
+
+ in >> name; m->gobble(in);
+ in >> parent1; m->gobble(in);
+
+ if (name == "Name") { //name = "Name" because we append the header line each time we add results from the groups
+ line = m->getline(in); m->gobble(in);
+ }else {
+ if (parent1 == "no") {
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ //is this sequence really not chimeric??
+ itChimeras = chimerasInFile.find(itUnique->second);
+
+ if (itChimeras == chimerasInFile.end()) {
+ //is this sequence not already in the file
+ itNames = namesInFile.find((itUnique->second));
+
+ if (itNames == namesInFile.end()) { out << itUnique->second << '\t' << "no" << endl; namesInFile.insert(itUnique->second); }
+ }
+ }
+ }else { //read the rest of the line
+ double DivQLAQRB,PerIDQLAQRB,BootStrapA,DivQLBQRA,PerIDQLBQRA,BootStrapB;
+ string flag, range1, range2;
+ bool print = false;
+ in >> parent2 >> DivQLAQRB >> PerIDQLAQRB >> BootStrapA >> DivQLBQRA >> PerIDQLBQRA >> BootStrapB >> flag >> range1 >> range2; m->gobble(in);
+
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ name = itUnique->second;
+ //is this name already in the file
+ itNames = namesInFile.find((name));
+
+ if (itNames == namesInFile.end()) { //no not in file
+ if (flag == "no") { //are you really a no??
+ //is this sequence really not chimeric??
+ itChimeras = chimerasInFile.find(name);
+
+ //then you really are a no so print, otherwise skip
+ if (itChimeras == chimerasInFile.end()) { print = true; }
+
+ }else{ print = true; }
+ }
+ }
+
+ if (print) {
+ out << name << '\t';
+
+ namesInFile.insert(name);
+
+ //output parent1's name
+ itUnique = uniqueNames.find(parent1);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << '\t'; }
+
+ //output parent2's name
+ itUnique = uniqueNames.find(parent2);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << '\t'; }
+
+ out << DivQLAQRB << '\t' << PerIDQLAQRB << '\t' << BootStrapA << '\t' << DivQLBQRA << '\t' << PerIDQLBQRA << '\t' << BootStrapB << '\t' << flag << '\t' << range1 << '\t' << range2 << endl;
+ }
+ }
+ }
+ }
+ in.close();
+ out.close();
+
+ m->mothurRemove(outputFileName);
+ rename((outputFileName+".temp").c_str(), outputFileName.c_str());
+
+ //edit fasta file
+ if (trim) {
+ ifstream in3;
+ m->openInputFile(trimFileName, in3);
+
+ ofstream out3;
+ m->openOutputFile(trimFileName+".temp", out3);
+
+ namesInFile.clear();
+
+ while (!in3.eof()) {
+ if (m->control_pressed) { in3.close(); out3.close(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); m->mothurRemove((trimFileName+".temp")); return 0; }
+
+ Sequence seq(in3); m->gobble(in3);
+
+ if (seq.getName() != "") {
+ //find unique name
+ itUnique = uniqueNames.find(seq.getName());
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ seq.getName() + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ itNames = namesInFile.find((itUnique->second));
+
+ if (itNames == namesInFile.end()) {
+ seq.printSequence(out3);
+ }
+ }
+ }
+ }
+ in3.close();
+ out3.close();
+
+ m->mothurRemove(trimFileName);
+ rename((trimFileName+".temp").c_str(), trimFileName.c_str());
+ }
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "deconvoluteResults");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ChimeraSlayerCommand::setUpForSelfReference(SequenceParser*& parser, map<string, string>& fileGroup, map<string, map<string, int> >& fileToPriority, int s){
+ try {
+ fileGroup.clear();
+ fileToPriority.clear();
+
+ string nameFile = "";
+ if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
+ nameFile = nameFileNames[s];
+ }else { nameFile = getNamesFile(fastaFileNames[s]); }
+
+ //you provided a groupfile
+ string groupFile = "";
+ if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; }
+
+ if (groupFile == "") {
+ if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
+
+ //sort fastafile by abundance, returns new sorted fastafile name
+ m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
+ priority = sortFastaFile(fastaFileNames[s], nameFile);
+ m->mothurOut("Done."); m->mothurOutEndLine();
+
+ fileToPriority[fastaFileNames[s]] = priority;
+ fileGroup[fastaFileNames[s]] = "noGroup";
+ }else {
+ //Parse sequences by group
+ parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+ vector<string> groups = parser->getNamesOfGroups();
+
+ for (int i = 0; i < groups.size(); i++) {
+ vector<Sequence> thisGroupsSeqs = parser->getSeqs(groups[i]);
+ map<string, string> thisGroupsMap = parser->getNameMap(groups[i]);
+ group2NameMap[groups[i]] = thisGroupsMap;
+ string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta";
+ priority = sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile);
+ fileToPriority[newFastaFile] = priority;
+ fileGroup[newFastaFile] = groups[i];
+ }
+ }
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "setUpForSelfReference");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ChimeraSlayerCommand::setUpForSelfReference(SequenceCountParser*& parser, map<string, string>& fileGroup, map<string, map<string, int> >& fileToPriority, int s){
+ try {
+ fileGroup.clear();
+ fileToPriority.clear();
+
+ string nameFile = "";
+ if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
+ nameFile = nameFileNames[s];
+ }else { m->control_pressed = true; return 0; }
+
+ CountTable ct;
+ if (!ct.testGroups(nameFile)) {
+ if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
+
+ //sort fastafile by abundance, returns new sorted fastafile name
+ m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
+ priority = sortFastaFile(fastaFileNames[s], nameFile);
+ m->mothurOut("Done."); m->mothurOutEndLine();
+
+ fileToPriority[fastaFileNames[s]] = priority;
+ fileGroup[fastaFileNames[s]] = "noGroup";
+ }else {
+ //Parse sequences by group
+ parser = new SequenceCountParser(nameFile, fastaFileNames[s]);
+ vector<string> groups = parser->getNamesOfGroups();
+
+ for (int i = 0; i < groups.size(); i++) {
+ vector<Sequence> thisGroupsSeqs = parser->getSeqs(groups[i]);
+ map<string, int> thisGroupsMap = parser->getCountTable(groups[i]);
+ string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta";
+ sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile);
+ fileToPriority[newFastaFile] = thisGroupsMap;
+ fileGroup[newFastaFile] = groups[i];
+ }
+ }
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "setUpForSelfReference");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChimeraSlayerCommand::getNamesFile(string& inputFile){
+ try {
+ string nameFile = "";
+
+ m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ //use unique.seqs to create new name and fastafile
+ string inputString = "fasta=" + inputFile;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* uniqueCommand = new DeconvoluteCommand(inputString);
+ uniqueCommand->execute();
+
+ map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
+
+ delete uniqueCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ nameFile = filenames["name"][0];
+ inputFile = filenames["fasta"][0];
+
+ return nameFile;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "getNamesFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ChimeraSlayerCommand::driverGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist){
+ try {
+ int totalSeqs = 0;
+ ofstream outCountList;
+
+ if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }
+
+ for (map<string, map<string, int> >::iterator itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) {
+
+ if (m->control_pressed) { return 0; }
+
+ int start = time(NULL);
+ string thisFastaName = itFile->first;
+ map<string, int> thisPriority = itFile->second;
+ string thisoutputFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.chimera";
+ string thisaccnosFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.accnos";
+ string thistrimFastaFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.fasta";
+
+ m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
+
+ lines.clear();
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int proc = 1;
+ vector<unsigned long long> positions = m->divideFile(thisFastaName, proc);
+ lines.push_back(linePair(positions[0], positions[1]));
+#else
+ lines.push_back(linePair(0, 1000));
+#endif
+ int numSeqs = driver(lines[0], thisoutputFileName, thisFastaName, thisaccnosFileName, thistrimFastaFileName, thisPriority);
+
+ //if we provided a count file with group info and set dereplicate=t, then we want to create a *.pick.count_table
+ //This table will zero out group counts for seqs determined to be chimeric by that group.
+ if (dups) {
+ if (!m->isBlank(thisaccnosFileName)) {
+ ifstream in;
+ m->openInputFile(thisaccnosFileName, in);
+ string name;
+ if (hasCount) {
+ while (!in.eof()) {
+ in >> name; m->gobble(in);
+ outCountList << name << '\t' << fileGroup[thisFastaName] << endl;
+ }
+ in.close();
+ }else {
+ map<string, map<string, string> >::iterator itGroupNameMap = group2NameMap.find(fileGroup[thisFastaName]);
+ if (itGroupNameMap != group2NameMap.end()) {
+ map<string, string> thisnamemap = itGroupNameMap->second;
+ map<string, string>::iterator itN;
+ ofstream out;
+ m->openOutputFile(thisaccnosFileName+".temp", out);
+ while (!in.eof()) {
+ in >> name; m->gobble(in);
+ itN = thisnamemap.find(name);
+ if (itN != thisnamemap.end()) {
+ vector<string> tempNames; m->splitAtComma(itN->second, tempNames);
+ for (int j = 0; j < tempNames.size(); j++) { out << tempNames[j] << endl; }
+
+ }else { m->mothurOut("[ERROR]: parsing cannot find " + name + ".\n"); m->control_pressed = true; }
+ }
+ out.close();
+ in.close();
+ m->renameFile(thisaccnosFileName+".temp", thisaccnosFileName);
+ }else { m->mothurOut("[ERROR]: parsing cannot find " + fileGroup[thisFastaName] + ".\n"); m->control_pressed = true; }
+ }
+
+ }
+ }
+
+ //append files
+ m->appendFiles(thisoutputFileName, outputFName); m->mothurRemove(thisoutputFileName);
+ m->appendFiles(thisaccnosFileName, accnos); m->mothurRemove(thisaccnosFileName);
+ if (trim) { m->appendFiles(thistrimFastaFileName, fasta); m->mothurRemove(thistrimFastaFileName); }
+ m->mothurRemove(thisFastaName);
+
+ totalSeqs += numSeqs;
+
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
+ }
+
+ if (hasCount && dups) { outCountList.close(); }
+
+ return totalSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "driverGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist, string countFile) {
+ try {
+ int process = 1;
+ int num = 0;
+ processIDS.clear();
+
+ if (fileToPriority.size() < processors) { processors = fileToPriority.size(); }
+
+ CountTable newCount;
+ if (hasCount && dups) { newCount.readTable(countFile, true); }
+
+ int groupsPerProcessor = fileToPriority.size() / processors;
+ int remainder = fileToPriority.size() % processors;
+
+ vector< map<string, map<string, int> > > breakUp;
+
+ for (int i = 0; i < processors; i++) {
+ map<string, map<string, int> > thisFileToPriority;
+ map<string, map<string, int> >::iterator itFile;
+ int count = 0;
+ int enough = groupsPerProcessor;
+ if (i == 0) { enough = groupsPerProcessor + remainder; }
+
+ for (itFile = fileToPriority.begin(); itFile != fileToPriority.end();) {
+ thisFileToPriority[itFile->first] = itFile->second;
+ fileToPriority.erase(itFile++);
+ count++;
+ if (count == enough) { break; }
+ }
+ breakUp.push_back(thisFileToPriority);
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", breakUp[process], fileGroup, accnos + toString(getpid()) + ".byCount");
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputFName + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup, accnos + ".byCount");
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = outputFName + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); m->mothurRemove(tempFile);
+ }
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the slayerData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<slayerData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for(int i=1; i<processors; i++ ){
+ string extension = toString(i) + ".temp";
+ slayerData* tempslayer = new slayerData(group2NameMap, hasCount, dups, (accnos + toString(i) +".byCount"), (outputFName + extension), (fasta + extension), (accnos + extension), templatefile, search, blastlocation, trimera, trim, realign, m, breakUp[i], fileGroup, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
+ pDataArray.push_back(tempslayer);
+ processIDS.push_back(i);
+
+ //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i-1] = CreateThread(NULL, 0, MySlayerGroupThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup, accnos + ".byCount");
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->fileToPriority.size() != pDataArray[i]->end) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->end) + " of " + toString(pDataArray[i]->fileToPriority.size()) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+ //read my own
+ if (hasCount && dups) {
+ if (!m->isBlank(accnos + ".byCount")) {
+ ifstream in2;
+ m->openInputFile(accnos + ".byCount", in2);
+
+ string name, group;
+ while (!in2.eof()) {
+ in2 >> name >> group; m->gobble(in2);
+ newCount.setAbund(name, group, 0);
+ }
+ in2.close();
+ }
+ m->mothurRemove(accnos + ".byCount");
+ }
+
+
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
+ m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
+ m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
+
+ if (trim) {
+ m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
+ m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
+ }
+
+ if (hasCount && dups) {
+ if (!m->isBlank(accnos + toString(processIDS[i]) + ".byCount")) {
+ ifstream in2;
+ m->openInputFile(accnos + toString(processIDS[i]) + ".byCount", in2);
+
+ string name, group;
+ while (!in2.eof()) {
+ in2 >> name >> group; m->gobble(in2);
+ newCount.setAbund(name, group, 0);
+ }
+ in2.close();
+ }
+ m->mothurRemove(accnos + toString(processIDS[i]) + ".byCount");
+ }
+
+ }
+
+ //print new *.pick.count_table
+ if (hasCount && dups) { newCount.printTable(countlist); }
+
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "createProcessesGroups");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string filename, string accnos, string fasta, map<string, int>& priority){
+ try {
+
+ Chimera* chimera;
+ if (templatefile != "self") { //you want to run slayer with a reference template
+ chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
+ }else {
+ chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
+ }
+
+ if (m->control_pressed) { delete chimera; return 0; }
+
+ if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+ templateSeqsLength = chimera->getLength();
+
+ ofstream out;
+ m->openOutputFile(outputFName, out);
+
+ ofstream out2;
+ m->openOutputFile(accnos, out2);
+
+ ofstream out3;
+ if (trim) { m->openOutputFile(fasta, out3); }
+
+ ifstream inFASTA;
+ m->openInputFile(filename, inFASTA);
+
+ inFASTA.seekg(filePos.start);
+
+ if (filePos.start == 0) { chimera->printHeader(out); }
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { delete chimera; out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1; }
+
+ Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
+ string candidateAligned = candidateSeq->getAligned();
+
+ if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
+ if (candidateSeq->getAligned().length() != templateSeqsLength) {
+ m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
+ }else{
+ //find chimeras
+ chimera->getChimeras(candidateSeq);
+
+ if (m->control_pressed) { delete chimera; delete candidateSeq; return 1; }
+
+ //if you are not chimeric, then check each half
+ data_results wholeResults = chimera->getResults();
+
+ //determine if we need to split
+ bool isChimeric = false;
+
+ if (wholeResults.flag == "yes") {
+ string chimeraFlag = "no";
+ if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
+ ||
+ (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+
+
+ if (chimeraFlag == "yes") {
+ if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
+ }
+ }
+
+ if ((!isChimeric) && trimera) {
+
+ //split sequence in half by bases
+ string leftQuery, rightQuery;
+ Sequence tempSeq(candidateSeq->getName(), candidateAligned);
+ divideInHalf(tempSeq, leftQuery, rightQuery);
+
+ //run chimeraSlayer on each piece
+ Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
+ Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
+
+ //find chimeras
+ chimera->getChimeras(left);
+ data_results leftResults = chimera->getResults();
+
+ chimera->getChimeras(right);
+ data_results rightResults = chimera->getResults();
+
+ //if either piece is chimeric then report
+ Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
+ if (trim) { trimmed.printSequence(out3); }
+
+ delete left; delete right;
+
+ }else { //already chimeric
+ //print results
+ Sequence trimmed = chimera->print(out, out2);
+ if (trim) { trimmed.printSequence(out3); }
+ }
+
+
+ }
+ count++;
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos.end)) { break; }
+ #else
+ if (inFASTA.eof()) { break; }
+ #endif
+
+ delete candidateSeq;
+ //report progress
+ if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
+ }
+ //report progress
+ if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+ "\n"); }
+
+ int numNoParents = chimera->getNumNoParents();
+ if (numNoParents == count) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+
+ out.close();
out2.close();
if (trim) { out3.close(); }
inFASTA.close();
+ delete chimera;
return count;
+
+
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayerCommand", "driver");
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
- try {
+int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, set<string>& cnames, vector<unsigned long long>& MPIPos, string filename, map<string, int>& priority, bool byGroup){
+ try {
MPI_Status status;
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ Chimera* chimera;
+ if (templatefile != "self") { //you want to run slayer with a reference template
+ chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
+ }else {
+ chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand(), byGroup);
+ }
+
+ if (m->control_pressed) { delete chimera; return 0; }
+
+ if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+ templateSeqsLength = chimera->getLength();
+
for(int i=0;i<num;i++){
- if (m->control_pressed) { return 1; }
+ if (m->control_pressed) { delete chimera; return 1; }
//read next sequence
int length = MPIPos[start+i+1] - MPIPos[start+i];
delete buf4;
Sequence* candidateSeq = new Sequence(iss); m->gobble(iss);
+ string candidateAligned = candidateSeq->getAligned();
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
//find chimeras
chimera->getChimeras(candidateSeq);
- if (m->control_pressed) { delete candidateSeq; return 1; }
-
- //print results
- Sequence* trimmed = chimera->print(outMPI, outAccMPI);
+ if (m->control_pressed) { delete chimera; delete candidateSeq; return 1; }
+
+ //if you are not chimeric, then check each half
+ data_results wholeResults = chimera->getResults();
- if (trim) {
- string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
- delete trimmed;
+ //determine if we need to split
+ bool isChimeric = false;
+
+ if (wholeResults.flag == "yes") {
+ string chimeraFlag = "no";
+ if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
+ ||
+ (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
- //write to accnos file
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
- MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
+ if (chimeraFlag == "yes") {
+ if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
+ }
}
- //do you want to check both pieces for chimeras
- //if (trimera) {}
+ if ((!isChimeric) && trimera) {
+ //split sequence in half by bases
+ string leftQuery, rightQuery;
+ Sequence tempSeq(candidateSeq->getName(), candidateAligned);
+ divideInHalf(tempSeq, leftQuery, rightQuery);
+
+ //run chimeraSlayer on each piece
+ Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
+ Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
+
+ //find chimeras
+ chimera->getChimeras(left);
+ data_results leftResults = chimera->getResults();
+
+ chimera->getChimeras(right);
+ data_results rightResults = chimera->getResults();
+
+ //if either piece is chimeric then report
+ bool flag = false;
+ Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults, flag);
+ if (flag) { cnames.insert(candidateSeq->getName()); }
+
+ if (trim) {
+ string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
+
+ //write to accnos file
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+
+ MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+ }
+ delete left; delete right;
+
+ }else {
+ //print results
+ Sequence trimmed = chimera->print(outMPI, outAccMPI);
+ cnames.insert(candidateSeq->getName());
+
+ if (trim) {
+ string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
+
+ //write to accnos file
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+
+ MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+ }
+ }
+
}
}
delete candidateSeq;
//report progress
- if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; }
}
//report progress
- if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); }
+ if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; }
-
+ int numNoParents = chimera->getNumNoParents();
+ if (numNoParents == num) { cout << "[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors." << endl; }
+
+ delete chimera;
return 0;
}
catch(exception& e) {
/**************************************************************************************************/
-int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) {
+int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta, map<string, int>& thisPriority) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
int num = 0;
+ processIDS.clear();
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp");
+ num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", thisPriority);
//pass numSeqs to parent
ofstream out;
m->openOutputFile(tempFile, out);
out << num << endl;
out.close();
-
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
ifstream in;
string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
- if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
- in.close(); remove(tempFile.c_str());
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); m->mothurRemove(tempFile);
}
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the slayerData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<slayerData*> pDataArray;
+ DWORD dwThreadIdArray[processors];
+ HANDLE hThreadArray[processors];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors; i++ ){
+ string extension = toString(i) + ".temp";
+ slayerData* tempslayer = new slayerData((outputFileName + extension), (fasta + extension), (accnos + extension), filename, templatefile, search, blastlocation, trimera, trim, realign, m, lines[i].start, lines[i].end, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
+ pDataArray.push_back(tempslayer);
+ processIDS.push_back(i);
+
+ //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
+ rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+ rename((accnos + toString(processIDS[0]) + ".temp").c_str(), accnos.c_str());
+ if (trim) { rename((fasta + toString(processIDS[0]) + ".temp").c_str(), fasta.c_str()); }
+
+ //append output files
+ for(int i=1;i<processIDS.size();i++){
+ m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
+ m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
+ m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
+
+ if (trim) {
+ m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
+ m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
+ }
+ }
+
return num;
-#endif
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
/**************************************************************************************************/
+int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
+ try {
+
+ string queryUnAligned = querySeq.getUnaligned();
+ int numBases = int(queryUnAligned.length() * 0.5);
+
+ string queryAligned = querySeq.getAligned();
+ leftQuery = querySeq.getAligned();
+ rightQuery = querySeq.getAligned();
+
+ int baseCount = 0;
+ int leftSpot = 0;
+ for (int i = 0; i < queryAligned.length(); i++) {
+ //if you are a base
+ if (isalpha(queryAligned[i])) {
+ baseCount++;
+ }
+
+ //if you have half
+ if (baseCount >= numBases) { leftSpot = i; break; } //first half
+ }
+
+ //blank out right side
+ for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
+
+ //blank out left side
+ for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
+ try {
+ map<string, int> nameAbund;
+
+ //read through fastafile and store info
+ map<string, string> seqs;
+ ifstream in;
+ m->openInputFile(fastaFile, in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return nameAbund; }
+
+ Sequence seq(in); m->gobble(in);
+ seqs[seq.getName()] = seq.getAligned();
+ }
+
+ in.close();
+
+ //read namefile or countfile
+ vector<seqPriorityNode> nameMapCount;
+ int error;
+ if (hasCount) {
+ CountTable ct;
+ ct.readTable(nameFile, true);
+
+ for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
+ int num = ct.getNumSeqs(it->first);
+ if (num == 0) { error = 1; }
+ else {
+ seqPriorityNode temp(num, it->second, it->first);
+ nameMapCount.push_back(temp);
+ }
+ }
+ }else { error = m->readNames(nameFile, nameMapCount, seqs); }
+
+ if (m->control_pressed) { return nameAbund; }
+
+ if (error == 1) { m->control_pressed = true; return nameAbund; }
+ if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return nameAbund; }
+
+ sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
+
+ string newFasta = fastaFile + ".temp";
+ ofstream out;
+ m->openOutputFile(newFasta, out);
+
+ //print new file in order of
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
+ nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical;
+ }
+ out.close();
+
+ rename(newFasta.c_str(), fastaFile.c_str());
+
+ return nameAbund;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<string, int> ChimeraSlayerCommand::sortFastaFile(vector<Sequence>& thisseqs, map<string, string>& nameMap, string newFile) {
+ try {
+ map<string, int> nameAbund;
+ vector<seqPriorityNode> nameVector;
+
+ //read through fastafile and store info
+ map<string, string> seqs;
+
+ for (int i = 0; i < thisseqs.size(); i++) {
+
+ if (m->control_pressed) { return nameAbund; }
+
+ map<string, string>::iterator itNameMap = nameMap.find(thisseqs[i].getName());
+
+ if (itNameMap == nameMap.end()){
+ m->control_pressed = true;
+ m->mothurOut("[ERROR]: " + thisseqs[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
+ }else {
+ int num = m->getNumNames(itNameMap->second);
+
+ seqPriorityNode temp(num, thisseqs[i].getAligned(), thisseqs[i].getName());
+ nameVector.push_back(temp);
+ }
+ }
+
+ //sort by num represented
+ sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
+
+ if (m->control_pressed) { return nameAbund; }
+
+ if (thisseqs.size() != nameVector.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return nameAbund; }
+
+ ofstream out;
+ m->openOutputFile(newFile, out);
+
+ //print new file in order of
+ for (int i = 0; i < nameVector.size(); i++) {
+ out << ">" << nameVector[i].name << endl << nameVector[i].seq << endl;
+ nameAbund[nameVector[i].name] = nameVector[i].numIdentical;
+ }
+ out.close();
+
+ return nameAbund;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int ChimeraSlayerCommand::sortFastaFile(vector<Sequence>& thisseqs, map<string, int>& countMap, string newFile) {
+ try {
+ vector<seqPriorityNode> nameVector;
+
+ //read through fastafile and store info
+ map<string, string> seqs;
+
+ for (int i = 0; i < thisseqs.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ map<string, int>::iterator itCountMap = countMap.find(thisseqs[i].getName());
+
+ if (itCountMap == countMap.end()){
+ m->control_pressed = true;
+ m->mothurOut("[ERROR]: " + thisseqs[i].getName() + " is in your fastafile, but is not in your count file, please correct."); m->mothurOutEndLine();
+ }else {
+ seqPriorityNode temp(itCountMap->second, thisseqs[i].getAligned(), thisseqs[i].getName());
+ nameVector.push_back(temp);
+ }
+ }
+
+ //sort by num represented
+ sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
+
+ if (m->control_pressed) { return 0; }
+
+ if (thisseqs.size() != nameVector.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your count file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+
+ ofstream out;
+ m->openOutputFile(newFile, out);
+
+ //print new file in order of
+ for (int i = 0; i < nameVector.size(); i++) {
+ out << ">" << nameVector[i].name << endl << nameVector[i].seq << endl;
+ }
+ out.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
projects / mothur.git / blobdiff