//
#include "sracommand.h"
+#include "sffinfocommand.h"
+#include "parsefastaqcommand.h"
//**********************************************************************************************************************
vector<string> SRACommand::setParameters(){
try {
- CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","sra",false,false); parameters.push_back(psff);
- CommandParameter pfastqfile("fastqfile", "InputTypes", "", "", "none", "none", "none","sra",false,false); parameters.push_back(pfastqfile);
+ CommandParameter psff("sff", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(psff);
+ CommandParameter pgroup("group", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter pfile("file", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfile);
+ CommandParameter pfastq("fastq", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfastq);
//choose only one multiple options
CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform);
+ 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);
+
//every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
string SRACommand::getHelpString(){
try {
string helpString = "";
- helpString += "The sra command creates a sequence read archive from sff or fastq files.\n";
- helpString += "The sra command parameters are: sff, fastqfiles, oligos, platform....\n";
- helpString += "The sffiles parameter is used to provide a file containing a \n";
+ helpString += "The sra command creates the necessary files for a NCBI submission. The xml file and individual sff or fastq files parsed from the original sff or fastq file.\n";
+ helpString += "The sra command parameters are: sff, fastq, file, oligos, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, group.\n";
+ helpString += "The sff parameter is used to provide the original sff file.\n";
+ helpString += "The fastq parameter is used to provide the original fastq file.\n";
+ helpString += "The oligos parameter is used to provide an oligos file to parse your sff or fastq file by.\n";
+ helpString += "The group parameter is used to provide the group file to parse your sff or fastq file by.\n";
+ helpString += "The file parameter is used to provide a file containing a list of individual fastq or sff files.\n";
+ helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
+ helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
+ helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
+ helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
+ helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
+
helpString += "The new command should be in the following format: \n";
helpString += "new(...)\n";
return helpString;
try {
string pattern = "";
- if (type == "sra") { pattern = "[filename],sra"; }
+ if (type == "xml") { pattern = "[filename],xml"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["sra"] = tempOutNames;
+ outputTypes["xml"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SRACommand", "SRACommand");
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ vector<string> tempOutNames;
+ outputTypes["xml"] = 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);
else {
string path;
- it = parameters.find("sfffiles");
+ it = parameters.find("sff");
//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["sfffiles"] = inputDir + it->second; }
+ if (path == "") { parameters["sff"] = inputDir + it->second; }
}
- it = parameters.find("fastqfiles");
+ it = parameters.find("fastq");
+ //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["fastq"] = inputDir + it->second; }
+ }
+
+ 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; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("oligos");
//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["fastqfiles"] = inputDir + it->second; }
+ if (path == "") { parameters["oligos"] = inputDir + it->second; }
}
}
//check for parameters
- fastqfiles = validParameter.validFile(parameters, "fastqfiles", true);
- if (fastqfiles == "not open") { fastqfiles = ""; abort = true; }
- else if (fastqfiles == "not found") { fastqfiles = ""; }
+ fastqfile = validParameter.validFile(parameters, "fastq", true);
+ if (fastqfile == "not open") { fastqfile = ""; abort = true; }
+ else if (fastqfile == "not found") { fastqfile = ""; }
- sfffiles = validParameter.validFile(parameters, "sfffiles", true);
- if (sfffiles == "not open") { sfffiles = ""; abort = true; }
- else if (sfffiles == "not found") { sfffiles = ""; }
+ sfffile = validParameter.validFile(parameters, "sff", true);
+ if (sfffile == "not open") { sfffile = ""; abort = true; }
+ else if (sfffile == "not found") { sfffile = ""; }
+
+ file = validParameter.validFile(parameters, "file", true);
+ if (file == "not open") { file = ""; abort = true; }
+ else if (file == "not found") { file = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ oligosfile = validParameter.validFile(parameters, "oligos", true);
+ if (oligosfile == "not found") { oligosfile = ""; }
+ else if(oligosfile == "not open") { abort = true; }
+ else { m->setOligosFile(oligosfile); }
+
+
+ file = validParameter.validFile(parameters, "file", true);
+ if (file == "not open") { file = ""; abort = true; }
+ else if (file == "not found") { file = ""; }
- if ((fastqfiles == "") && (sfffiles == "")) {
- m->mothurOut("No valid current files. You must provide a sfffiles or fastqfiles file before you can use the sra command."); m->mothurOutEndLine(); abort = true;
+ if ((fastqfile == "") && (sfffile == "") && (sfffile == "")) {
+ m->mothurOut("[ERROR]: You must provide a file, sff file or fastq file before you can use the sra command."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (oligosfile != "")) {
+ m->mothurOut("[ERROR]: You may not use a group file and an oligos file, only one."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((fastqfile != "") || (sfffile != "")) {
+ if ((groupfile == "") && (oligosfile == "")) {
+ oligosfile = m->getOligosFile();
+ if (oligosfile != "") { m->mothurOut("Using " + oligosfile + " as input file for the oligos parameter."); m->mothurOutEndLine(); }
+ else {
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("[ERROR]: You must provide groupfile or oligos file if splitting a fastq or sff file."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
}
//use only one Mutliple type
if ((platform == "454") || (platform == "????") || (platform == "????") || (platform == "????")) { }
else { m->mothurOut("Not a valid platform option. Valid platform options are 454, ...."); m->mothurOutEndLine(); abort = true; }
+
+ string temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
+
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
}
}
}
//**********************************************************************************************************************
-
int SRACommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+ //parse files
+ vector<string> filesBySample;
+ isSFF = false;
+
+ if (file != "") { readFile(filesBySample); }
+ else if (sfffile != "") { parseSffFile(filesBySample); }
+ else if (fastqfile != "") { parseFastqFile(filesBySample); }
+
+ //create xml file
+
//output files created by command
m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
+int SRACommand::readFile(vector<string>& files){
+ try {
+ files.clear();
+
+ ifstream in;
+ m->openInputFile(file, in);
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string filename;
+ in >> filename; m->gobble(in);
+ files.push_back(filename);
+ }
+ in.close();
+
+ if (!m->control_pressed) {
+ if (files.size() > 0) {
+ int pos = files[0].find(".sff");
+ if (pos != string::npos) { isSFF = true; } //these files are sff files
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SRACommand::parseSffFile(vector<string>& files){
+ try {
+ isSFF = true;
+ //run sffinfo to parse sff file into individual sampled sff files
+ string commandString = "sff=" + sfffile;
+ if (groupfile != "") { commandString += ", group=" + groupfile; }
+ else if (oligosfile != "") {
+ commandString += ", oligos=" + oligosfile;
+ //add in pdiffs, bdiffs, ldiffs, sdiffs, tdiffs
+ if (pdiffs != 0) { commandString += ", pdiffs=" + toString(pdiffs); }
+ if (bdiffs != 0) { commandString += ", bdiffs=" + toString(bdiffs); }
+ if (ldiffs != 0) { commandString += ", ldiffs=" + toString(ldiffs); }
+ if (sdiffs != 0) { commandString += ", sdiffs=" + toString(sdiffs); }
+ if (tdiffs != 0) { commandString += ", tdiffs=" + toString(tdiffs); }
+ }
+ m->mothurOutEndLine();
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: sffinfo(" + commandString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* sffinfoCommand = new SffInfoCommand(commandString);
+ sffinfoCommand->execute();
+
+ map<string, vector<string> > filenames = sffinfoCommand->getOutputFiles();
+ map<string, vector<string> >::iterator it = filenames.find("sff");
+ if (it != filenames.end()) { files = it->second; }
+ else { m->control_pressed = true; } // error in sffinfo
+
+ delete sffinfoCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readFile");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int SRACommand::parseFastqFile(vector<string>& files){
+ try {
+
+ //run sffinfo to parse sff file into individual sampled sff files
+ string commandString = "fastq=" + fastqfile;
+ if (groupfile != "") { commandString += ", group=" + groupfile; }
+ else if (oligosfile != "") {
+ commandString += ", oligos=" + oligosfile;
+ //add in pdiffs, bdiffs, ldiffs, sdiffs, tdiffs
+ if (pdiffs != 0) { commandString += ", pdiffs=" + toString(pdiffs); }
+ if (bdiffs != 0) { commandString += ", bdiffs=" + toString(bdiffs); }
+ if (ldiffs != 0) { commandString += ", ldiffs=" + toString(ldiffs); }
+ if (sdiffs != 0) { commandString += ", sdiffs=" + toString(sdiffs); }
+ if (tdiffs != 0) { commandString += ", tdiffs=" + toString(tdiffs); }
+ }
+ m->mothurOutEndLine();
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: fastq.info(" + commandString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* fastqinfoCommand = new ParseFastaQCommand(commandString);
+ fastqinfoCommand->execute();
+
+ map<string, vector<string> > filenames = fastqinfoCommand->getOutputFiles();
+ map<string, vector<string> >::iterator it = filenames.find("fastq");
+ if (it != filenames.end()) { files = it->second; }
+ else { m->control_pressed = true; } // error in sffinfo
+
+ delete fastqinfoCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
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