#else
uchimeCommand = "\"" + uchimeCommand + "\"";
#endif
-
- char* tempUchime;
+ char* tempUchime;
tempUchime= new char[uchimeCommand.length()+1];
*tempUchime = '\0';
strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
cPara.push_back(tempUchime);
- char* tempIn = new char[8];
- *tempIn = '\0'; strncat(tempIn, "--input", 7);
- //strcpy(tempIn, "--input");
- cPara.push_back(tempIn);
- char* temp = new char[filename.length()+1];
- *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
- //strcpy(temp, filename.c_str());
- cPara.push_back(temp);
-
- //are you using a reference file
+ //are you using a reference file
if (templatefile != "self") {
+ string outputFileName = filename.substr(1, filename.length()-2) + ".uchime_formatted";
+ prepFile(filename.substr(1, filename.length()-2), outputFileName);
+ filename = outputFileName;
+ filename = "\"" + filename + "\"";
//add reference file
char* tempRef = new char[5];
//strcpy(tempRef, "--db");
cPara.push_back(tempR);
}
+ char* tempIn = new char[8];
+ *tempIn = '\0'; strncat(tempIn, "--input", 7);
+ //strcpy(tempIn, "--input");
+ cPara.push_back(tempIn);
+ char* temp = new char[filename.length()+1];
+ *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
+ //strcpy(temp, filename.c_str());
+ cPara.push_back(temp);
+
char* tempO = new char[12];
*tempO = '\0'; strncat(tempO, "--uchimeout", 11);
//strcpy(tempO, "--uchimeout");
in.close();
out.close();
+ //if (templatefile != "self") { m->mothurRemove(filename); }
+
return num;
}
catch(exception& e) {
}
}
/**************************************************************************************************/
+//uchime can't handle some of the things allowed in mothurs fasta files. This functions "cleans up" the file.
+int ChimeraUchimeCommand::prepFile(string filename, string output) {
+ try {
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ ofstream out;
+ m->openOutputFile(output, out);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") { seq.printSequence(out); }
+ }
+ in.close();
+ out.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraUchimeCommand", "prepFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename, string accnos, string alns, int& numChimeras) {
try {
int deconvoluteResults(map<string, string>&, string, string, string);
int driverGroups(string, string, string, string, int, int, vector<string>);
int createProcessesGroups(string, string, string, string, vector<string>, string, string, string);
+ int prepFile(string filename, string);
};
strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
cPara.push_back(tempUchime);
- char* tempIn = new char[8];
- *tempIn = '\0'; strncat(tempIn, "--input", 7);
- //strcpy(tempIn, "--input");
- cPara.push_back(tempIn);
- char* temp = new char[filename.length()+1];
- *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
- //strcpy(temp, filename.c_str());
- cPara.push_back(temp);
-
- //add reference file
+ string outputFileName = filename.substr(1, filename.length()-2) + ".uchime_formatted";
+ //prepFile(filename.substr(1, filename.length()-2), outputFileName);
+ //prepFile(filename, outputFileName);
+ /******************************************/
+ ifstream in23;
+ m->openInputFile((filename.substr(1, filename.length()-2)), in23);
+
+ ofstream out23;
+ m->openOutputFile(outputFileName, out23);
+
+ while (!in23.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in23); m->gobble(in23);
+
+ if (seq.getName() != "") { seq.printSequence(out23); }
+ }
+ in23.close();
+ out23.close();
+ /******************************************/
+
+ filename = outputFileName;
+ filename = "\"" + filename + "\"";
+
+ //add reference file
char* tempRef = new char[5];
//strcpy(tempRef, "--db");
*tempRef = '\0'; strncat(tempRef, "--db", 4);
//strcpy(tempR, templatefile.c_str());
*tempR = '\0'; strncat(tempR, templatefile.c_str(), templatefile.length());
cPara.push_back(tempR);
+
+ char* tempIn = new char[8];
+ *tempIn = '\0'; strncat(tempIn, "--input", 7);
+ //strcpy(tempIn, "--input");
+ cPara.push_back(tempIn);
+ char* temp = new char[filename.length()+1];
+ *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
+ //strcpy(temp, filename.c_str());
+ cPara.push_back(temp);
char* tempO = new char[12];
*tempO = '\0'; strncat(tempO, "--uchimeout", 11);
--- /dev/null
+//
+// sffmultiplecommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 8/14/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "sffmultiplecommand.h"
+
+
+//**********************************************************************************************************************
+vector<string> SffMultipleCommand::setParameters(){
+ try {
+ CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfile);
+
+ //sffinfo
+ CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
+
+ //trim.flows
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
+ CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
+ CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
+ CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
+ CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
+
+ 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, "SffMultipleCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SffMultipleCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The sff.multiple command reads a file containing sff filenames and optional oligos filenames. It runs the files through sffinfo, trim.flows, shhh.flows and trim.seqs combining the results.\n";
+ helpString += "The sff.multiple command parameters are file, trim, maxhomop, maxflows, minflows, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, signal, noise, allfiles, order. file is required. \n";
+ helpString += "The file parameter allows you to enter the a file containing the list of sff files and optional oligos files.\n";
+ helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores generated by sffinfo trimmed to the clipQualLeft and clipQualRight values. Default=True. \n";
+ helpString += "Example sff.multiple(file=mySffOligosFile.txt, trim=F).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. file), '=' and parameters (i.e.mySffOligosFile.txt).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SffMultipleCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ //if (type == "fasta") { outputFileName = "fasta"; }
+ //else if (type == "flow") { outputFileName = "flow"; }
+ // else if (type == "sfftxt") { outputFileName = "sff.txt"; }
+ //else if (type == "qfile") { outputFileName = "qual"; }
+ //else {
+ m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;
+ //}
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+SffMultipleCommand::SffMultipleCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "SffMultipleCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+SffMultipleCommand::SffMultipleCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ //valid paramters for this command
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("file");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["file"] = inputDir + it->second; }
+ }
+ }
+
+ filename = validParameter.validFile(parameters, "file", true);
+ if (filename == "not open") { filename = ""; abort = true; }
+ else if (filename == "not found") { filename = ""; }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
+ trim = m->isTrue(temp);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "SffMultipleCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffMultipleCommand::execute(){
+ try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ vector<string> sffFiles, oligosFiles;
+ readFile(sffFiles, oligosFiles);
+
+ if (m->control_pressed) { return 0; }
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("qfile");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+ }
+
+ itTypes = outputTypes.find("flow");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
+ }
+
+ //report output filenames
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffMultipleCommand::readFile(vector<string>& sffFiles, vector<string>& oligosFiles){
+ try {
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ string oligos, sff;
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ in >> sff;
+
+ //ignore file pairing
+ if(sff[0] == '#'){ while (!in.eof()) { char c = in.get(); if (c == 10 || c == 13){ break; } } m->gobble(in); }
+ else { //check for oligos file
+ oligos = "";
+
+ // get rest of line in case there is a oligos filename
+ while (!in.eof()) {
+ char c = in.get();
+ if (c == 10 || c == 13){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { oligos += c; }
+ }
+ }
+ m->gobble(in);
+
+ sffFiles.push_back(sff);
+ oligosFiles.push_back(oligos); //will push a blank if there is not an oligos for this sff file
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "readFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
+
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