//
#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);
+ CommandParameter pcontact("contact", "InputTypes", "", "", "none", "none", "none","xml",false,true,true); parameters.push_back(pcontact);
//choose only one multiple options
- CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform);
+ CommandParameter pplatform("platform", "Multiple", "_LS454-ILLUMINA-ION_TORRENT-PACBIO_SMRT", "_LS454", "", "", "","",false,false); parameters.push_back(pplatform);
+ CommandParameter pinstrument("instrument", "Multiple", "454_GS-454_GS_20-454_GS_FLX-454_GS_FLX_Titanium-454_GS_Junior-Illumina_Genome_Analyzer-Illumina_Genome_Analyzer_II-Illumina_Genome_Analyzer_IIx-Illumina_HiSeq_2000-Illumina_HiSeq_1000-Illumina_MiSeq-PacBio_RS-Ion_Torrent_PGM-unspecified", "454_GS", "", "", "","",false,false); parameters.push_back(pinstrument);
+ CommandParameter plibstrategy("libstrategy", "String", "AMPLICON", "", "", "", "","",false,false); parameters.push_back(plibstrategy);
+ CommandParameter plibsource("libsource", "String", "METAGENOMIC", "", "", "", "","",false,false); parameters.push_back(plibsource);
+ CommandParameter plibselection("libselection", "String", "PCR", "", "", "", "","",false,false); parameters.push_back(plibselection);
+
+ 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 new command should be in the following format: \n";
- helpString += "new(...)\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, contact, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, group, platform, libstrategy, libsource, libselection and instrument.\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 contact parameter is used to provide your contact 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 or paired fastq files with a group assignment. File lines can be 2 or 3 columns. The 2 column files are sff file then oligos or fastqfile then oligos. You may have multiple lines in the file. The 3 column files are for paired read libraries. The format is groupName, forwardFastqFile reverseFastqFile.\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 platform parameter is used to specify platfrom you are using choices are: _LS454,ILLUMINA,ION_TORRENT,PACBIO_SMRT. Default=_LS454. This is a controlled vocabulary section in the XML file that will be generated.\n";
+ helpString += "The instrument parameter is used to specify instrument. Choices are 454_GS-454_GS_20-454_GS_FLX-454_GS_FLX_Titanium-454_GS_Junior-Illumina_Genome_Analyzer-Illumina_Genome_Analyzer_II-Illumina_Genome_Analyzer_IIx-Illumina_HiSeq_2000-Illumina_HiSeq_1000-Illumina_MiSeq-PacBio_RS-Ion_Torrent_PGM-unspecified. Default=454_GS. This is a controlled vocabulary section in the XML file that will be generated. \n";
+ helpString += "The libstrategy parameter is used to specify library strategy. Default=AMPLICON. Choices are AMPLICON,WGA,WGS,WGX,RNA-Seq,miRNA-Seq,WCS,CLONE,POOLCLONE,CLONEEND,FINISHING,ChIP-Seq,MNase-Seq,DNase-Hypersensitivity,Bisulfite-Seq,Tn-Seq,EST,FL-cDNA,CTS,MRE-Seq,MeDIP-Seq,MBD-Seq,OTHER. This is a controlled vocabulary section in the XML file that will be generated. \n";
+ helpString += "The libsource parameter is used to specify library source. Default=METAGENOMIC. Choices are METAGENOMIC,GENOMIC,TRANSCRIPTOMIC,METATRANSCRIPTOMIC,SYNTHETIC,VIRAL_RNA,OTHER. This is a controlled vocabulary section in the XML file that will be generated. \n";
+ helpString += "The libselection parameter is used to specify library selection. Default=PCR. Choices are PCR,RANDOM,RANDOM_PCR,RT-PCR,HMPR,MF,CF-S,CF-H,CF-T,CF-M,MDA,MSLL,cDNA,ChIP,MNase,DNAse,Hybrid_Selection,Reduced_Representation,Restriction_Digest,5-methylcytidine_antibody,MBD2_protein_methyl-CpG_binding_domain,CAGE,RACE,size_fractionation,Padlock_probes_capture_method,other,unspecified. This is a controlled vocabulary section in the XML file that will be generated. \n";
+
+ helpString += "The sra should be in the following format: \n";
+ helpString += "sra(...)\n";
return helpString;
}
catch(exception& e) {
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");
SRACommand::SRACommand(string option) {
try {
abort = false; calledHelp = false;
+ libLayout = "single"; //controlled vocab
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
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; }
+ }
+
+ it = parameters.find("contact");
+ //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["contact"] = 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); }
+
+ contactfile = validParameter.validFile(parameters, "contact", true);
+ if (contactfile == "not found") { contactfile = ""; m->mothurOut("[ERROR]: You must provide a contact file before you can use the sra command."); m->mothurOutEndLine(); abort = true; }
+ else if(contactfile == "not open") { abort = true; }
+
+ 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
- platform = validParameter.validFile(parameters, "platform", false);
- if (platform == "not found") { platform = "454"; }
+ //use only one Mutliple type _LS454-ILLUMINA-ION_TORRENT-PACBIO_SMRT
+ platform = validParameter.validFile(parameters, "platform", false); if (platform == "not found") { platform = "_LS454"; }
+ if (!checkCasesPlatforms(platform)) { abort = true; } //error message in function
+
+ if (!abort) { //don't check instrument model is platform is bad
+ //454_GS-454_GS_20-454_GS_FLX-454_GS_FLX_Titanium-454_GS_Junior-Illumina_Genome_Analyzer-Illumina_Genome_Analyzer_II-Illumina_Genome_Analyzer_IIx-Illumina_HiSeq_2000-Illumina_HiSeq_1000-Illumina_MiSeq-PacBio_RS-Ion_Torrent_PGM-unspecified
+ instrumentModel = validParameter.validFile(parameters, "instrument", false); if (instrumentModel == "not found") { instrumentModel = "454_GS"; }
+ if (!checkCasesInstrumentModels(instrumentModel)) { abort = true; } //error message in function
+ }
+ //turn _ to spaces mothur's work around
+ for (int i = 0; i < instrumentModel.length(); i++) { if (instrumentModel[i] == '_') { instrumentModel[i] = ' '; } }
+
+ libStrategy = validParameter.validFile(parameters, "libstrategy", false); if (libStrategy == "not found") { libStrategy = "AMPLICON"; }
+ if (!checkCasesLibStrategy(libStrategy)) { abort = true; } //error message in function
+
+ //turn _ to spaces mothur's work around
+ for (int i = 0; i < libStrategy.length(); i++) { if (libStrategy[i] == '_') { libStrategy[i] = ' '; } }
+
+ libSource = validParameter.validFile(parameters, "libsource", false); if (libSource == "not found") { libSource = "METAGENOMIC"; }
+ if (!checkCasesLibSource(libSource)) { abort = true; } //error message in function
+
+ //turn _ to spaces mothur's work around
+ for (int i = 0; i < libSource.length(); i++) { if (libSource[i] == '_') { libSource[i] = ' '; } }
+
+ libSelection = validParameter.validFile(parameters, "libselection", false); if (libSelection == "not found") { libSelection = "PCR"; }
+ if (!checkCasesLibSelection(libSelection)) { abort = true; } //error message in function
+
+ //turn _ to spaces mothur's work around
+ for (int i = 0; i < libSelection.length(); i++) { if (libSelection[i] == '_') { libSelection[i] = ' '; } }
+
+
+ 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);
- if ((platform == "454") || (platform == "????") || (platform == "????") || (platform == "????")) { }
- else { m->mothurOut("Not a valid platform option. Valid platform options are 454, ...."); m->mothurOutEndLine(); abort = true; }
+ 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; }
-
+ readContactFile();
+ if (oligosfile != "") { readOligos(); Groups.push_back("scrap"); }
+ if (groupfile != "") { GroupMap groupmap(groupfile); groupmap.readMap(); Groups = groupmap.getNamesOfGroups(); Groups.push_back("scrap"); }
+
+ if (m->control_pressed) { return 0; }
+
+ //parse files
+ map<string, vector<string> > filesBySample;
+ isSFF = false;
+
+ if (file != "") { readFile(filesBySample); }
+ else if (sfffile != "") { parseSffFile(filesBySample); }
+ else if (fastqfile != "") { parseFastqFile(filesBySample); }
+
+ //checks groups and files returned from parse - removes any groups that did not get reads assigned to them, orders files.
+ checkGroups(filesBySample);
+
+ //create xml file
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(inputfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(inputfile));
+ string outputFileName = getOutputFileName("xml", variables);
+ outputNames.push_back(outputFileName); outputTypes["xml"].push_back(outputFileName);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ //contacts portion
+ ////////////////////////////////////////////////////////
+ out << "<Submission>\n";
+ out << "\t<Description>\n";
+ out << "\t\t<Comment> New Submission. Generated by mothur version " + m->getVersion() + " </Comment> \n";
+ out << "\t\t<Submitter user_name=\"" + submissionName + "\"/>\n";
+ out << "\t\t<Organization type=\"" + centerType + "\">\n";
+ out << "\t\t<Name>" + centerName + "</Name>\n";
+ out << "\t\t<Contact> email=\"" + email + "\">\n";
+ out << "\t\t\t<Name>\n";
+ out << "\t\t\t\t<First>" + firstName + "</First>\n";
+ out << "\t\t\t\t<Last>" + firstName + "</Last>\n";
+ out << "\t\t\t</Name>\n";
+ out << "\t\t</Contact>\n";
+ out << "\t\t</Organization>\n";
+ out << "\t</Description>\n";
+ ////////////////////////////////////////////////////////
+
+ //bioproject
+ ////////////////////////////////////////////////////////
+ out << "\t<Action>\n";
+ out << "\t\t<AddData target_db=\"BioProject\">\n";
+ out << "\t\t\t<Data content_type=\"XML\">\n";
+ out << "\t\t\t\t<XmlContent>\n";
+ out << "\t\t\t\t\t<Project schema_version=\"2.0\">\n";
+ out << "\t\t\t\t\t\t<ProjectID>\n";
+ ///////////////////////out << "\t\t\t\t\t\t<SPUID spuid_namespace=\"Institute name\">" + ProjectID + " </SPUID> \n";
+ out << "\t\t\t\t\t\t</ProjectID>\n";
+ out << "\t\t\t\t\t\t<Descriptor>\n";
+ ////////////////////out << "\t\t\t\t\t\t\t<Title>" + title + " </Title> \n";
+ out << "\t\t\t\t\t\t\t<Description><p>" + description + "</p></Description> \n";
+ out << "\t\t\t\t\t\t\t<ExternalLink label=\"Website name\">\n";
+ /////////////////////////out << "\t\t\t\t\t\t\t\t<URL>" + website + "</URL>\n";
+ out << "\t\t\t\t\t\t\t</ExternalLink>\n";
+ out << "\t\t\t\t\t\t\t<Relevance>\n";
+ //////////////////////out << "\t\t\t\t\t\t\t\t<Medical>" + medicalRelevance + "</Medical>\n";
+ out << "\t\t\t\t\t\t\t</Relevance>\n";
+ out << "\t\t\t\t\t\t</Descriptor>\n";
+ out << "\t\t\t\t\t\t<ProjectType>\n";
+ /////////////////////////out << "\t\t\t\t\t\t\t<ProjectTypeSubmission sample_scope=\"eMultiisolate\">\n"; //<!-- controlled vocabulary? -->
+ out << "\t\t\t\t\t\t\t\t<Organism>\n";
+ ////////////////////out << "\t\t\t\t\t\t\t\t\t<OrganismName>" + scientificName + " </OrganismName> \n";
+ out << "\t\t\t\t\t\t\t\t</Organism>\n";
+ out << "\t\t\t\t\t\t\t\t<IntendedDataTypeSet>\n";
+ ////////////////////out << "\t\t\t\t\t\t\t\t\t<DataType>" + dataType + " </DataType> \n"; <!-- controlled vocabulary? -->
+ out << "\t\t\t\t\t\t\t\t</IntendedDataTypeSet>\n";
+ out << "\t\t\t\t\t\t\t</ProjectTypeSubmission>\n";
+ out << "\t\t\t\t\t\t</ProjectType>\n";
+ out << "\t\t\t\t\t</Project>\n";
+ out << "\t\t\t\t</XmlContent>\n";
+ out << "\t\t\t</Data>\n";
+ out << "\t\t\t<Identifier>\n";
+ ////////////////////////////out << "\t\t\t\t<SPUID spuid_namespace=\"Institute name\">" + ProjectID + " </SPUID>\n";
+ out << "\t\t\t</Identifier>\n";
+ out << "\t\t</AddData>\n";
+ out << "\t</Action>\n";
+ ////////////////////////////////////////////////////////
+
+ //bioSample
+ ////////////////////////////////////////////////////////
+ for (int i = 0; i < Groups.size(); i++) {
+
+ vector<string> thisGroupsFiles = filesBySample[Groups[i]];
+ string barcodeForThisSample = Group2Barcode[Groups[i]];
+
+ for (int j = 0; j < thisGroupsFiles.size(); j++) {
+ if (m->control_pressed) { break; }
+ out << "\t<Action>\n";
+ out << "\t\t<AddData target_db=\"BioSample\">\n";
+ out << "\t\t\t<Data content_type=\"XML\">\n";
+ out << "\t\t\t\t<XmlContent>\n";
+ out << "\t\t\t\t\t<BioSample schema_version=\"2.0\">\n";
+ out << "\t\t\t\t\t\t<SampleId>\n";
+ out << "\t\t\t\t\t\t<SPUID spuid_namespace=\"Institute name\">" + Groups[i] + " </SPUID> \n";
+ out << "\t\t\t\t\t\t</SampleId>\n";
+ out << "\t\t\t\t\t\t<Descriptor>\n";
+ ////////////////////out << "\t\t\t\t\t\t\t<Title>" + title + " </Title> \n";
+ out << "\t\t\t\t\t\t</Descriptor>\n";
+ out << "\t\t\t\t\t\t<Organism>\n";
+ ////////////////////out << "\t\t\t\t\t\t\t<OrganismName>" + scientificName + " </OrganismName> \n";
+ out << "\t\t\t\t\t\t</Organism>\n";
+ out << "\t\t\t\t\t\t<BioProject>\n";
+ ///////////////////////out << "\t\t\t\t\t\t\t<SPUID spuid_namespace=\"Institute name\">" + BioProject + " </SPUID> \n";
+ out << "\t\t\t\t\t\t</BioProject>\n";
+ out << "\t\t\t\t\t\t<Package>MIMARKS.specimen</Package>n";
+ out << "\t\t\t\t\t\t<Attributes>n";
+ //add biosample required attributes
+ ///////////////////////////////////////////////////////////////////////
+
+ out << "\t\t\t\t\t\t</Attributes>n";
+ out << "\t\t\t\t\t</BioSample>\n";
+ out << "\t\t\t\t</XmlContent>\n";
+ out << "\t\t\t</Data>\n";
+
+ //libID
+ out << "\t\t\t<Identifier>\n";
+ string libId = thisGroupsFiles[j] + barcodeForThisSample;
+ if (libLayout == "paired") { //adjust the libID because the thisGroupsFiles[j] contains two filenames
+ vector<string> pieces = m->splitWhiteSpace(thisGroupsFiles[j]);
+ libId = pieces[0] + barcodeForThisSample;
+ }
+ out << "\t\t\t\t<SPUID spuid_namespace=\"Institute name\">" + libId + " </SPUID>\n";
+ out << "\t\t\t</Identifier>\n";
+
+ out << "\t\t</AddData>\n";
+ out << "\t</Action>\n";
+ }
+ }
+
+ for (int i = 0; i < Groups.size(); i++) {
+
+ vector<string> thisGroupsFiles = filesBySample[Groups[i]];
+ string barcodeForThisSample = Group2Barcode[Groups[i]];
+
+ for (int j = 0; j < thisGroupsFiles.size(); j++) {
+ if (m->control_pressed) { break; }
+ out << "\t<Action>\n";
+ out << "\t\t<AddFiles target_db=\"SRA\">\n";
+ if (libLayout == "paired") { //adjust the libID because the thisGroupsFiles[j] contains two filenames
+ vector<string> pieces = m->splitWhiteSpace(thisGroupsFiles[j]);
+ out << "\t\t\t<File file_path=\"" + pieces[0] + "\">\n";
+ ////////////////////out << "\t\t\t\t<DataType>fastq</DataType> \n"; //since its paired we know its fastq, is the dataType the fileType???
+ out << "\t\t\t</File>\n";
+ out << "\t\t\t<File file_path=\"" + pieces[1] + "\">\n";
+ ////////////////////out << "\t\t\t\t<DataType>fastq</DataType> \n"; //since its paired we know its fastq, is the dataType the fileType???
+ out << "\t\t\t</File>\n";
+ }else { //single
+ out << "\t\t\t<File file_path=\"" + thisGroupsFiles[j] + "\">\n";
+ string dataType = "fastq";
+ if (isSFF) { dataType = "sff"; }
+ ////////////////////out << "\t\t\t\t<DataType>" + dataType + " </DataType> \n"; //is the dataType the fileType???
+ out << "\t\t\t</File>\n";
+ }
+ //attributes
+ out << "\t\t\t<Attribute name=\"instrument_model\">" + instrumentModel + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_strategy\">" + libStrategy + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_source\">" + libSource + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_selection\">" + libSelection + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_layout\">" + libLayout + "</Attribute>\n";
+
+ //////////////////bioSample info
+ ///////////////////bioProject info
+
+ //libID
+ out << "\t\t\t<Identifier>\n";
+ string libId = thisGroupsFiles[j] + barcodeForThisSample;
+ if (libLayout == "paired") { //adjust the libID because the thisGroupsFiles[j] contains two filenames
+ vector<string> pieces = m->splitWhiteSpace(thisGroupsFiles[j]);
+ libId = pieces[0] + barcodeForThisSample;
+ }
+ out << "\t\t\t\t<SPUID spuid_namespace=\"Institute name\">" + libId + " </SPUID>\n";
+ out << "\t\t\t</Identifier>\n";
+ out << "\t\t</AddFiles>\n";
+ out << "\t</Action>\n";
+ }
+ }
+
+ ////////////////////////////////////////////////////////
+ out << "</Submission>\n";
+ out.close();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output files created by command
m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
+int SRACommand::readContactFile(){
+ try {
+ lastName = ""; firstName = ""; submissionName = ""; email = ""; centerName = ""; centerType = ""; description = "";
+
+ ifstream in;
+ m->openInputFile(contactfile, in);
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string key, value;
+ in >> key; m->gobble(in);
+ value = m->getline(in); m->gobble(in);
+
+ for (int i = 0; i < key.length(); i++) { key[i] = toupper(key[i]); }
+
+ if (key == "USERNAME") { submissionName = value; }
+ else if (key == "LAST") { lastName = value; }
+ else if (key == "FIRST") { firstName = value; }
+ else if (key == "EMAIL") { email = value; }
+ else if (key == "CENTER") { centerName = value; }
+ else if (key == "TYPE") {
+ centerType = value;
+ for (int i = 0; i < centerType.length(); i++) { centerType[i] = tolower(centerType[i]); }
+ if ((centerType == "consortium") || (centerType == "center") || (centerType == "institute") || (centerType == "lab")) {}
+ else { m->mothurOut("[ERROR]: " + centerType + " is not a center type option. Valid center type options are consortium, center, institute and lab. This is a controlled vocabulary section in the XML file that will be generated."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }else if (key == "DESCRIPTION") { description = value; }
+ }
+ in.close();
+
+ if (lastName == "") { m->mothurOut("[ERROR]: missing last name from contacts file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (firstName == "") { m->mothurOut("[ERROR]: missing first name from contacts file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (submissionName == "") { m->mothurOut("[ERROR]: missing submission name from contacts file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (email == "") { m->mothurOut("[ERROR]: missing email from contacts file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (centerName == "") { m->mothurOut("[ERROR]: missing center name from contacts file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (centerType == "") { m->mothurOut("[ERROR]: missing center type from contacts file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (description == "") { m->mothurOut("[ERROR]: missing description from contacts file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readContactFile");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+// going to have to rework this to allow for other options --
+/*
+ file option 1
+
+ sfffile1 oligosfile1
+ sfffile2 oligosfile2
+ ...
+
+ file option 2
+
+ fastqfile1 oligosfile1
+ fastqfile2 oligosfile2
+ ...
+
+ file option 3
+
+ fastqfile fastqfile group
+ fastqfile fastqfile group
+ fastqfile fastqfile group
+ ...
+
+*/
+
+int SRACommand::readFile(map<string, vector<string> >& files){
+ try {
+ vector<string> theseFiles;
+ inputfile = file;
+ files.clear();
+
+ ifstream in;
+ m->openInputFile(file, in);
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { return 0; }
+
+ string line = m->getline(in); m->gobble(in);
+ vector<string> pieces = m->splitWhiteSpace(line);
+
+ string group = "";
+ string thisFileName1, thisFileName2; thisFileName1 = ""; thisFileName2 = "";
+ if (pieces.size() == 2) {
+ thisFileName1 = pieces[0];
+ thisFileName2 = pieces[1];
+ }else if (pieces.size() == 3) {
+ thisFileName1 = pieces[1];
+ thisFileName2 = pieces[2];
+ string group = pieces[0];
+ libLayout = "paired";
+ }else {
+ m->mothurOut("[ERROR]: file lines can be 2 or 3 columns. The 2 column files are sff file then oligos or fastqfile then oligos. You may have multiple lines in the file. The 3 column files are for paired read libraries. The format is groupName, forwardFastqFile reverseFastqFile. \n"); m->control_pressed = true;
+ }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", thisFileName1 = " + thisFileName1 + ", thisFileName2 = " + thisFileName2 + ".\n"); }
+
+ //check to make sure both are able to be opened
+ ifstream in2;
+ int openForward = m->openInputFile(thisFileName1, in2, "noerror");
+
+ //if you can't open it, try default location
+ if (openForward == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(thisFileName1);
+ m->mothurOut("Unable to open " + thisFileName1 + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in3;
+ openForward = m->openInputFile(tryPath, in3, "noerror");
+ in3.close();
+ thisFileName1 = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (openForward == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(thisFileName1);
+ m->mothurOut("Unable to open " + thisFileName1 + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openForward = m->openInputFile(tryPath, in4, "noerror");
+ thisFileName1 = tryPath;
+ in4.close();
+ }
+ }
+
+ if (openForward == 1) { //can't find it
+ m->mothurOut("[WARNING]: can't find " + thisFileName1 + ", ignoring.\n");
+ }else{ in2.close(); }
+
+ ifstream in3;
+ int openReverse = m->openInputFile(thisFileName2, in3, "noerror");
+
+ //if you can't open it, try default location
+ if (openReverse == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(thisFileName2);
+ m->mothurOut("Unable to open " + thisFileName2 + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in3;
+ openReverse = m->openInputFile(tryPath, in3, "noerror");
+ in3.close();
+ thisFileName2 = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (openReverse == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(thisFileName2);
+ m->mothurOut("Unable to open " + thisFileName2 + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openReverse = m->openInputFile(tryPath, in4, "noerror");
+ thisFileName2 = tryPath;
+ in4.close();
+ }
+ }
+
+ if (openReverse == 1) { //can't find it
+ m->mothurOut("[WARNING]: can't find " + thisFileName2 + ", ignoring pair.\n");
+ }else{ in3.close(); }
+
+
+
+ if ((pieces.size() == 2) && (openForward != 1) && (openReverse != 1)) { //good pair and sff or fastq and oligos
+ //process pair
+ int pos = theseFiles[0].find(".sff");
+ if (pos != string::npos) {//these files are sff files
+ isSFF = true;
+ sfffile = thisFileName1; oligosfile = thisFileName2;
+ readOligos();
+ parseSffFile(files);
+ }else{
+ isSFF = false;
+ fastqfile = thisFileName1; oligosfile = thisFileName2;
+ readOligos();
+ parseFastqFile(files);
+ }
+
+ }else if((pieces.size() == 3) && (openForward != 1) && (openReverse != 1)) { //good pair and paired read
+ map<string, vector<string> >::iterator it = files.find(group);
+ if (it == files.end()) {
+ vector<string> temp; temp.push_back(thisFileName1 + " " + thisFileName2); files[group] = temp;
+ }else {
+ files[group].push_back(thisFileName1 + " " + thisFileName2);
+ }
+ }
+ }
+ in.close();
+
+ inputfile = file;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SRACommand::parseSffFile(map<string, vector<string> >& files){
+ try {
+ vector<string> theseFiles;
+ inputfile = sfffile;
+ libLayout = "single"; //controlled vocab
+
+ 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()) { theseFiles = it->second; }
+ else { m->control_pressed = true; } // error in sffinfo
+
+ delete sffinfoCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ mapGroupToFile(files, theseFiles);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readFile");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int SRACommand::parseFastqFile(map<string, vector<string> >& files){
+ try {
+ vector<string> theseFiles;
+ inputfile = fastqfile;
+ libLayout = "single"; //controlled vocab
+
+ //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()) { theseFiles = it->second; }
+ else { m->control_pressed = true; } // error in sffinfo
+
+ delete fastqinfoCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ mapGroupToFile(files, theseFiles);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readFile");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+//maps group to file
+int SRACommand::mapGroupToFile(map<string, vector<string> >& files, vector<string> theseFiles){
+ try {
+
+ for (int i = 0; i < Groups.size(); i++) {
+
+ set<int> matches;
+ for (int j = 0; j < theseFiles.size(); j++) {
+ int pos = theseFiles[j].find(Groups[i]);
+ if (pos != string::npos) { //you have a potential match, make sure you dont have a case of partial name
+ if (theseFiles[j][pos+Groups[i].length()] == '.') { //final.soil.sff vs final.soil2.sff both would match soil.
+ matches.insert(i);
+ }
+ }
+ }
+
+ if(matches.size() == 1) {
+ map<string, vector<string> >::iterator it = files.find(Groups[i]);
+ if (it == files.end()) {
+ vector<string> temp; temp.push_back(theseFiles[*matches.begin()]); files[Groups[i]] = temp;
+ }else {
+ files[Groups[i]].push_back(theseFiles[*matches.begin()]);
+ }
+ }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkGroups");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+//checks groups and files returned from parse - removes any groups that did not get reads assigned to them, orders files.
+int SRACommand::checkGroups(map<string, vector<string> >& files){
+ try {
+ vector<string> newGroups;
+ for (int i = 0; i < Groups.size(); i++) {
+
+ map<string, vector<string> >::iterator it = files.find(Groups[i]);
+ //no files for this group, remove it
+ if (it == files.end()) { }
+ else { newGroups.push_back(Groups[i]); }
+ }
+
+ Groups = newGroups;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkGroups");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int SRACommand::readOligos(){
+ try {
+ ifstream inOligos;
+ m->openInputFile(oligosfile, inOligos);
+
+ string type, oligo, roligo, group;
+ bool hasPrimer = false; bool hasPairedBarcodes = false; pairedOligos = false;
+
+ int indexPrimer = 0;
+ int indexBarcode = 0;
+ int indexPairedPrimer = 0;
+ int indexPairedBarcode = 0;
+ set<string> uniquePrimers;
+ set<string> uniqueBarcodes;
+
+ while(!inOligos.eof()){
+
+ inOligos >> type;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
+
+ if(type[0] == '#'){
+ while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ m->gobble(inOligos);
+ }
+ else{
+ m->gobble(inOligos);
+ //make type case insensitive
+ for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
+
+ inOligos >> oligo;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
+
+ for(int i=0;i<oligo.length();i++){
+ oligo[i] = toupper(oligo[i]);
+ if(oligo[i] == 'U') { oligo[i] = 'T'; }
+ }
+
+ if(type == "FORWARD"){
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ //check for repeat barcodes
+ map<string, int>::iterator itPrime = primers.find(oligo);
+ if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); } }
+
+ primers[oligo] = indexPrimer; indexPrimer++;
+ primerNameVector.push_back(group);
+ }
+ else if (type == "PRIMER"){
+ m->gobble(inOligos);
+
+ inOligos >> roligo;
+
+ for(int i=0;i<roligo.length();i++){
+ roligo[i] = toupper(roligo[i]);
+ if(roligo[i] == 'U') { roligo[i] = 'T'; }
+ }
+ roligo = reverseOligo(roligo);
+
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ oligosPair newPrimer(oligo, roligo);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
+
+ //check for repeat barcodes
+ string tempPair = oligo+roligo;
+ if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine(); }
+ else { uniquePrimers.insert(tempPair); }
+
+ if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
+
+ pairedPrimers[indexPairedPrimer]=newPrimer; indexPairedPrimer++;
+ primerNameVector.push_back(group);
+ hasPrimer = true;
+ }
+ else if(type == "REVERSE"){
+ //Sequence oligoRC("reverse", oligo);
+ //oligoRC.reverseComplement();
+ string oligoRC = reverseOligo(oligo);
+ revPrimer.push_back(oligoRC);
+ }
+ else if(type == "BARCODE"){
+ inOligos >> group;
+
+ //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
+ //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
+
+ string temp = "";
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { temp += c; }
+ }
+
+ //then this is illumina data with 4 columns
+ if (temp != "") {
+ hasPairedBarcodes = true;
+ string reverseBarcode = group; //reverseOligo(group); //reverse barcode
+ group = temp;
+
+ for(int i=0;i<reverseBarcode.length();i++){
+ reverseBarcode[i] = toupper(reverseBarcode[i]);
+ if(reverseBarcode[i] == 'U') { reverseBarcode[i] = 'T'; }
+ }
+
+ reverseBarcode = reverseOligo(reverseBarcode);
+ oligosPair newPair(oligo, reverseBarcode);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
+ //check for repeat barcodes
+ string tempPair = oligo+reverseBarcode;
+ if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding."); m->mothurOutEndLine(); }
+ else { uniqueBarcodes.insert(tempPair); }
+
+ pairedBarcodes[indexPairedBarcode]=newPair; indexPairedBarcode++;
+ barcodeNameVector.push_back(group);
+ }else {
+ //check for repeat barcodes
+ map<string, int>::iterator itBar = barcodes.find(oligo);
+ if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ barcodes[oligo]=indexBarcode; indexBarcode++;
+ barcodeNameVector.push_back(group);
+ }
+ }else if(type == "LINKER"){
+ linker.push_back(oligo);
+ }else if(type == "SPACER"){
+ spacer.push_back(oligo);
+ }
+ else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
+ }
+ m->gobble(inOligos);
+ }
+ inOligos.close();
+
+ if (hasPairedBarcodes || hasPrimer) {
+ pairedOligos = true;
+ if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true; m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine(); return 0; }
+ }
+
+
+ //add in potential combos
+ if(barcodeNameVector.size() == 0){
+ barcodeNameVector.push_back("");
+ }
+
+ if(primerNameVector.size() == 0){
+ primerNameVector.push_back("");
+ }
+
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ if (pairedOligos) {
+ for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
+
+ string primerName = primerNameVector[itPrimer->first];
+ string barcodeName = barcodeNameVector[itBar->first];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastqFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->first];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->first];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ }
+ }
+ uniqueNames.insert(comboGroupName);
+ Group2Barcode[comboGroupName] = (itBar->second).forward+"."+(itBar->second).reverse;
+ }
+ }
+ }
+ }else {
+ for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = primerNameVector[itPrimer->second];
+ string barcodeName = barcodeNameVector[itBar->second];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastqFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ }
+ uniqueNames.insert(comboGroupName);
+ Group2Barcode[comboGroupName] = itBar->first;
+ }
+ }
+ }
+ }
+
+
+ if (m->debug) { int count = 0; for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { m->mothurOut("[DEBUG]: " + toString(count) + " groupName = " + *it + "\n"); count++; } }
+
+ for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { Groups.push_back(*it); }
+
+ return true;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readOligos");
+ exit(1);
+ }
+}
+//********************************************************************/
+string SRACommand::reverseOligo(string oligo){
+ try {
+ string reverse = "";
+
+ for(int i=oligo.length()-1;i>=0;i--){
+
+ if(oligo[i] == 'A') { reverse += 'T'; }
+ else if(oligo[i] == 'T'){ reverse += 'A'; }
+ else if(oligo[i] == 'U'){ reverse += 'A'; }
+
+ else if(oligo[i] == 'G'){ reverse += 'C'; }
+ else if(oligo[i] == 'C'){ reverse += 'G'; }
+
+ else if(oligo[i] == 'R'){ reverse += 'Y'; }
+ else if(oligo[i] == 'Y'){ reverse += 'R'; }
+
+ else if(oligo[i] == 'M'){ reverse += 'K'; }
+ else if(oligo[i] == 'K'){ reverse += 'M'; }
+
+ else if(oligo[i] == 'W'){ reverse += 'W'; }
+ else if(oligo[i] == 'S'){ reverse += 'S'; }
+
+ else if(oligo[i] == 'B'){ reverse += 'V'; }
+ else if(oligo[i] == 'V'){ reverse += 'B'; }
+
+ else if(oligo[i] == 'D'){ reverse += 'H'; }
+ else if(oligo[i] == 'H'){ reverse += 'D'; }
+
+ else { reverse += 'N'; }
+ }
+
+
+ return reverse;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "reverseOligo");
+ exit(1);
+ }
+}
+//********************************************************************/
+//_LS454-ILLUMINA-ION_TORRENT-PACBIO_SMRT
+bool SRACommand::checkCasesPlatforms(string& platform){
+ try {
+ string original = platform;
+ bool isOkay = true;
+
+ //remove users possible case errors
+ for (int i = 0; i < platform.size(); i++) { platform[i] = toupper(platform[i]); }
+
+ //_LS454-ILLUMINA-ION_TORRENT-PACBIO_SMRT
+
+ if ((platform == "_LS454") || (platform == "ILLUMINA") || (platform == "ION_TORRENT") || (platform == "PACBIO_SMRT") || (platform == "454")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+ if (platform == "454") { platform = "_LS454"; }
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid platform option. Valid platform options are _LS454, ILLUMINA-ION, TORRENT or PACBIO_SMRT."); m->mothurOutEndLine(); abort = true;
+ }
+
+ return isOkay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkCasesPlatforms");
+ exit(1);
+ }
+}
+//********************************************************************/
+//454_GS-454_GS_20-454_GS_FLX-454_GS_FLX_Titanium-454_GS_Junior-Illumina_Genome_Analyzer-Illumina_Genome_Analyzer_II-Illumina_Genome_Analyzer_IIx-Illumina_HiSeq_2000-Illumina_HiSeq_1000-Illumina_MiSeq-PacBio_RS-Ion_Torrent_PGM-unspecified
+bool SRACommand::checkCasesInstrumentModels(string& instrumentModel){
+ try {
+ string original = instrumentModel;
+ bool isOkay = true;
+
+ //remove users possible case errors
+ for (int i = 0; i < instrumentModel.size(); i++) { instrumentModel[i] = toupper(instrumentModel[i]); }
+
+ //_LS454-ILLUMINA-ION_TORRENT-PACBIO_SMRT
+ if (platform == "_LS454") { //instrument model options are 454_GS-454_GS_20-454_GS_FLX-454_GS_FLX_Titanium-454_GS_Junior-unspecified
+ if ((instrumentModel == "454_GS") || (instrumentModel == "454_GS_20") || (instrumentModel == "454_GS_FLX") || (instrumentModel == "454_GS_FLX_TITANIUM") || (instrumentModel == "454_GS_JUNIOR") || (instrumentModel == "UNSPECIFIED")) { }
+ else { isOkay = false; }
+ if (isOkay) {
+ if (instrumentModel == "454_GS_FLX_TITANIUM") { instrumentModel = "454_GS_FLX_Titanium"; }
+ if (instrumentModel == "454_GS_JUNIOR") { instrumentModel = "454_GS_Junior"; }
+ if (instrumentModel == "UNSPECIFIED") { instrumentModel = "unspecified"; }
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid instrument option for the " + platform + " platform. Valid instrument options are 454_GS, 454_GS_20, 454_GS_FLX, 454_GS_FLX_Titanium, 454_GS_Junior or unspecified."); m->mothurOutEndLine(); abort = true;
+ }
+
+ }else if (platform == "ILLUMINA") { //instrument model options are Illumina_Genome_Analyzer-Illumina_Genome_Analyzer_II-Illumina_Genome_Analyzer_IIx-Illumina_HiSeq_2000-Illumina_HiSeq_1000-Illumina_MiSeq-unspecified
+ if ((instrumentModel == "ILLUMINA_GENOME_ANALYZER") || (instrumentModel == "ILLUMINA_GENOME_ANALYZER_II") || (instrumentModel == "ILLUMINA_GENOME_ANALYZER_IIX") || (instrumentModel == "ILLUMINA_HISEQ_2000") || (instrumentModel == "ILLUMINA_HISEQ_1000") || (instrumentModel == "ILLUMINA_MISEQ") || (instrumentModel == "UNSPECIFIED")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+ if (instrumentModel == "ILLUMINA_GENOME_ANALYZER") { instrumentModel = "Illumina_Genome_Analyzer"; }
+ if (instrumentModel == "ILLUMINA_GENOME_ANALYZER_II") { instrumentModel = "Illumina_Genome_Analyzer_II"; }
+ if (instrumentModel == "ILLUMINA_GENOME_ANALYZER_IIX") { instrumentModel = "Illumina_Genome_Analyzer_IIx"; }
+ if (instrumentModel == "ILLUMINA_HISEQ_2000") { instrumentModel = "Illumina_HiSeq_2000"; }
+ if (instrumentModel == "ILLUMINA_HISEQ_1000") { instrumentModel = "Illumina_HiSeq_1000"; }
+ if (instrumentModel == "ILLUMINA_MISEQ") { instrumentModel = "Illumina_MiSeq"; }
+ if (instrumentModel == "UNSPECIFIED") { instrumentModel = "unspecified"; }
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid instrument option for the " + platform + " platform. Valid instrument options are Illumina_Genome_Analyzer, Illumina_Genome_Analyzer_II, Illumina_Genome_Analyzer_IIx, Illumina_HiSeq_2000, Illumina_HiSeq_1000, Illumina_MiSeq or unspecified."); m->mothurOutEndLine(); abort = true;
+ }
+
+ }else if (platform == "ION_TORRENT") { //instrument model options are Ion_Torrent_PGM-unspecified
+ if ((instrumentModel == "ION_TORRENT_PGM") || (instrumentModel == "UNSPECIFIED")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+ if (instrumentModel == "ION_TORRENT_PGM") { instrumentModel = "Ion_Torrent_PGM"; }
+ if (instrumentModel == "UNSPECIFIED") { instrumentModel = "unspecified"; }
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid instrument option for the " + platform + " platform. Valid instrument options are Ion_Torrent_PGM or unspecified."); m->mothurOutEndLine(); abort = true;
+ }
+ }else if (platform == "PACBIO_SMRT") { //instrument model options are PacBio_RS-unspecified
+ if ((instrumentModel == "PACBIO_RS") || (instrumentModel == "UNSPECIFIED")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+ if (instrumentModel == "PACBIO_RS") { instrumentModel = "PacBio_RS"; }
+ if (instrumentModel == "UNSPECIFIED") { instrumentModel = "unspecified"; }
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid instrument option for the " + platform + " platform. Valid instrument options are PacBio_RS or unspecified."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ return isOkay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkCasesInstrumentModels");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//AMPLICON,WGA,WGS,WGX,RNA-Seq,miRNA-Seq,WCS,CLONE,POOLCLONE,CLONEEND,FINISHING,ChIP-Seq,MNase-Seq,DNase-Hypersensitivity,Bisulfite-Seq,Tn-Seq,EST,FL-cDNA,CTS,MRE-Seq,MeDIP-Seq,MBD-Seq,OTHER
+bool SRACommand::checkCasesLibStrategy(string& libStrategy){
+ try {
+ string original = libStrategy;
+ bool isOkay = true;
+
+ //remove users possible case errors
+ for (int i = 0; i < libStrategy.size(); i++) { libStrategy[i] = toupper(libStrategy[i]); }
+
+ if ((libStrategy == "AMPLICON") || (libStrategy == "WGA") || (libStrategy == "WGS") || (libStrategy == "WGX") || (libStrategy == "RNA-SEQ") || (libStrategy == "MIRNA-SEQ") || (libStrategy == "WCS") || (libStrategy == "CLONE") || (libStrategy == "POOLCLONE") || (libStrategy == "CLONEEND") || (libStrategy == "FINISHING") || (libStrategy == "CHIP-SEQ") || (libStrategy == "MNASE-SEQ") || (libStrategy == "DNASE-HYPERSENSITIVITY") || (libStrategy == "BISULFITE-SEQ") || (libStrategy == "TN-SEQ") || (libStrategy == "EST") || (libStrategy == "FL-CDNA") || (libStrategy == "CTS") || (libStrategy == "MRE-SEQ")|| (libStrategy == "MEDIP-SEQ") || (libStrategy == "MBD-SEQ") || (libStrategy == "OTHER")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+ if (libStrategy == "RNA-SEQ") { libStrategy = "RNA-Seq"; }
+ if (libStrategy == "MIRNA-SEQ") { libStrategy = "miRNA-Seq"; }
+ if (libStrategy == "CHIP-SEQ") { libStrategy = "ChIP-Seq"; }
+ if (libStrategy == "MNASE-SEQ") { libStrategy = "MNase-Seq"; }
+ if (libStrategy == "DNASE-HYPERSENSITIVITY") { libStrategy = "DNase-Hypersensitivity"; }
+ if (libStrategy == "BISULFITE-SEQ") { libStrategy = "Bisulfite-Seq"; }
+ if (libStrategy == "TN-SEQ") { libStrategy = "Tn-Seq"; }
+ if (libStrategy == "FL-CDNA") { libStrategy = "FL-cDNA"; }
+ if (libStrategy == "MRE-SEQ") { libStrategy = "MRE-Seq"; }
+ if (libStrategy == "MEDIP-SEQ") { libStrategy = "MeDIP-Seq"; }
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid libstrategy option. Valid libstrategy options are AMPLICON,WGA,WGS,WGX,RNA-Seq,miRNA-Seq,WCS,CLONE,POOLCLONE,CLONEEND,FINISHING,ChIP-Seq,MNase-Seq,DNase-Hypersensitivity,Bisulfite-Seq,Tn-Seq,EST,FL-cDNA,CTS,MRE-Seq,MeDIP-Seq,MBD-Seq or OTHER."); m->mothurOutEndLine(); abort = true;
+ }
+
+ return isOkay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkCasesLibStrategy");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//METAGENOMIC,GENOMIC,TRANSCRIPTOMIC,METATRANSCRIPTOMIC,SYNTHETIC,VIRAL_RNA,OTHER
+bool SRACommand::checkCasesLibSource(string& libSource){
+ try {
+ string original = libSource;
+ bool isOkay = true;
+
+ //remove users possible case errors
+ for (int i = 0; i < libSource.size(); i++) { libSource[i] = toupper(libSource[i]); }
+
+ if ((libSource == "METAGENOMIC") || (libSource == "GENOMIC") || (libSource == "TRANSCRIPTOMIC") || (libSource == "METATRANSCRIPTOMIC") || (libSource == "SYNTHETIC") || (libSource == "VIRAL_RNA") || (libSource == "OTHER")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid libsource option. Valid libsource options are METAGENOMIC,GENOMIC,TRANSCRIPTOMIC,METATRANSCRIPTOMIC,SYNTHETIC,VIRAL_RNA or OTHER."); m->mothurOutEndLine(); abort = true;
+ }
+
+ return isOkay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkCasesLibStrategy");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//PCR,RANDOM,RANDOM_PCR,RT-PCR,HMPR,MF,CF-S,CF-H,CF-T,CF-M,MDA,MSLL,cDNA,ChIP,MNase,DNAse,Hybrid_Selection,Reduced_Representation,Restriction_Digest,5-methylcytidine_antibody,MBD2_protein_methyl-CpG_binding_domain,CAGE,RACE,size_fractionation,Padlock_probes_capture_method,other,unspecified
+bool SRACommand::checkCasesLibSelection(string& libSelection){
+ try {
+ string original = libSelection;
+ bool isOkay = true;
+
+ //remove users possible case errors
+ for (int i = 0; i < libSelection.size(); i++) { libSelection[i] = toupper(libSelection[i]); }
+
+ if ((libSelection == "PCR") || (libSelection == "RANDOM") || (libSelection == "RANDOM_PCR") || (libSelection == "RT-PCR") || (libSelection == "HMPR") || (libSelection == "MF") || (libSelection == "CF-S") || (libSelection == "CF-H") || (libSelection == "CF-T") || (libSelection == "CF-M") || (libSelection == "MDA") || (libSelection == "MSLL") || (libSelection == "CDNA") || (libSelection == "CHIP") || (libSelection == "MNASE") || (libSelection == "DNASE") || (libSelection == "HYBRID_SELECTION") || (libSelection == "REDUCED_REPRESENTATION") || (libSelection == "RESTRICTION_DIGEST") || (libSelection == "5-METHYLCYTIDINE_ANTIBODY") || (libSelection == "MBD2_PROTEIN_METHYL-CPG_BINDING_DOMAIN") || (libSelection == "CAGE") || (libSelection == "RACE") || (libSelection == "SIZE_FRACTIONATION") || (libSelection == "PADLOCK_PROBES_CAPTURE_METHOD") || (libSelection == "OTHER") || (libSelection == "UNSPECIFIED")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+ if (libSelection == "CDNA") { libSelection = "cDNA"; }
+ if (libSelection == "CHIP") { libSelection = "ChIP"; }
+ if (libSelection == "MNASE") { libSelection = "MNase"; }
+ if (libSelection == "DNASE") { libSelection = "DNAse"; }
+ if (libSelection == "HYBRID_SELECTION") { libSelection = "Hybrid_Selection"; }
+ if (libSelection == "REDUCED_REPRESENTATION") { libSelection = "Reduced_Representation"; }
+ if (libSelection == "RESTRICTION_DIGEST") { libSelection = "Restriction_Digest"; }
+ if (libSelection == "5-METHYLCYTIDINE_ANTIBODY") { libSelection = "5-methylcytidine_antibody"; }
+ if (libSelection == "MBD2_PROTEIN_METHYL-CPG_BINDING_DOMAIN") { libSelection = "MBD2_protein_methyl-CpG_binding_domain"; }
+ if (libSelection == "SIZE_FRACTIONATION") { libSelection = "size_fractionation"; }
+ if (libSelection == "PADLOCK_PROBES_CAPTURE_METHOD") { libSelection = "Padlock_probes_capture_method"; }
+ if (libSelection == "OTHER") { libSelection = "other"; }
+ if (libSelection == "UNSPECIFIED") { libSelection = "unspecified"; }
+
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid libselection option. Valid libselection options are PCR,RANDOM,RANDOM_PCR,RT-PCR,HMPR,MF,CF-S,CF-H,CF-T,CF-M,MDA,MSLL,cDNA,ChIP,MNase,DNAse,Hybrid_Selection,Reduced_Representation,Restriction_Digest,5-methylcytidine_antibody,MBD2_protein_methyl-CpG_binding_domain,CAGE,RACE,size_fractionation,Padlock_probes_capture_method,other or unspecified."); m->mothurOutEndLine(); abort = true;
+ }
+
+ return isOkay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkCasesLibSelection");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff