#include "filterseqscommand.h"
#include "sequence.hpp"
+
//**********************************************************************************************************************
-vector<string> FilterSeqsCommand::getValidParameters(){
+vector<string> FilterSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
+ CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
+ CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
+ CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ 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, "FilterSeqsCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-FilterSeqsCommand::FilterSeqsCommand(){
- try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["filter"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
+ m->errorOut(e, "FilterSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> FilterSeqsCommand::getRequiredParameters(){
+string FilterSeqsCommand::getHelpString(){
try {
- string Array[] = {"fasta"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n";
+ helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n";
+ helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n";
+ helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n";
+ helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n";
+ helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n";
+ helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n";
+ helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "The filter.seqs command should be in the following format: \n";
+ helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n";
+ helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "getRequiredParameters");
+ m->errorOut(e, "FilterSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> FilterSeqsCommand::getRequiredFiles(){
+FilterSeqsCommand::FilterSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["filter"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
exit(1);
}
}
/**************************************************************************************/
FilterSeqsCommand::FilterSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
filterFileName = "";
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ 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", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
fasta = validParameter.validFile(parameters, "fasta", false);
- if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true; }
+ if (fasta == "not found") {
+ fasta = m->getFastaFile();
+ if (fasta != "") { fastafileNames.push_back(fasta); m->mothurOut("Using " + fasta + " 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(fasta, 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]; }
- }
-
- ifstream in;
- int 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;
- }
- }
- //if you can't open it, try default location
- 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;
+ 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--;
}
}
- in.close();
+ 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]; }
+ }
+
+ ifstream in;
+ int 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--;
- }else{
- string simpleName = m->getSimpleName(fastafileNames[i]);
- filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ //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 you can't open it, try default location
+ 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{
+ string simpleName = m->getSimpleName(fastafileNames[i]);
+ filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ }
+ in.close();
}
- in.close();
}
//make sure there is at least one valid file left
temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
else { soft = (float)atoi(temp.c_str()) / 100.0; }
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
convert(temp, processors);
vertical = validParameter.validFile(parameters, "vertical", false);
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void FilterSeqsCommand::help(){
- try {
-
- m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
- m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n");
- m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
- m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
- m->mothurOut("The trump parameter .... The default is ...\n");
- m->mothurOut("The soft parameter .... The default is ....\n");
- m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
- m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
- m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
- m->mothurOut("The filter.seqs command should be in the following format: \n");
- m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
- m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "help");
- exit(1);
- }
-}
-
/**************************************************************************************/
int FilterSeqsCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
ifstream inFASTA;
m->openInputFile(fastafileNames[0], inFASTA);
m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
#ifdef USE_MPI
- int pid, start, end, numSeqsPerProcessor, num;
+ int pid, numSeqsPerProcessor, num;
int tag = 2001;
vector<unsigned long int>MPIPos;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_File outMPI;
- MPI_File tempMPI;
MPI_File inMPI;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
projects / mothur.git / blobdiff