*/
#include "makegroupcommand.h"
+#include "sequence.hpp"
+
+
+//**********************************************************************************************************************
+vector<string> MakeGroupCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
+ 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, "MakeGroupCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MakeGroupCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n";
+ helpString += "The make.group command parameters are fasta, groups and output. Fasta and group are required.\n";
+ helpString += "The output parameter allows you to specify the name of groupfile created. \n";
+ helpString += "The make.group command should be in the following format: \n";
+ helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n";
+ helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MakeGroupCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "group") { pattern = "[filename],groups"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MakeGroupCommand::MakeGroupCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//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 AlignArray[] = {"fasta","groups","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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 = ""; }
-
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["group"] = 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);
if (inputDir == "not found"){ inputDir = ""; }
-
fastaFileName = validParameter.validFile(parameters, "fasta", false);
- if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
- else {
- splitAtDash(fastaFileName, fastaFileNames);
+ if (fastaFileName == "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(fastaFileName, 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 = 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 = openInputFile(fastaFileNames[i], in);
- in.close();
-
- if (ableToOpen == 1) {
- m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
+ 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();
+ filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));
+ }
+ 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 (!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 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{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); m->setFastaFile(fastaFileNames[i]); }
+ }
}
+ //prevent giantic file name
+ map<string, string> variables;
+ variables["[filename]"] = filename;
+ if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; }
+ filename = getOutputFileName("group",variables);
+
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); 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 = ""; }
+
+ output = validParameter.validFile(parameters, "output", false);
+ if (output == "not found") { output = ""; }
+ else{ filename = output; }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
+ else { m->splitAtDash(groups, groupsNames); }
+
+ if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true; }
}
-
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-MakeGroupCommand::~MakeGroupCommand(){ }
-
-//**********************************************************************************************************************
-
-void MakeGroupCommand::help(){
- try {
- m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
- m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
- m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
- m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
- m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
- m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
- m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
- m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
- m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
- m->mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.\n");
- m->mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");
- m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
- m->mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
- m->mothurOut("The align.seqs command should be in the following format: \n");
- m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
- m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "MakeGroupCommand", "help");
- exit(1);
- }
-}
-
-
//**********************************************************************************************************************
int MakeGroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
+
+ filename = outputDir + filename;
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
+
+ ifstream in;
+ m->openInputFile(fastaFileNames[i], in);
+
+ while (!in.eof()) {
+
+ Sequence seq(in, "no align"); m->gobble(in);
+
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); m->mothurRemove(filename); return 0; }
+
+ if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; }
+ }
+ in.close();
+ }
+ out.close();
m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- //for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOut("Output File Names: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
m->mothurOutEndLine();
-
+
+ //set group file as new current groupfile
+ string current = "";
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
exit(1);
}
}
+//**********************************************************************************************************************
+
projects / mothur.git / blobdiff