//**********************************************************************************************************************
vector<string> SRACommand::setParameters(){
try {
- CommandParameter psff("sff", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","sra",false,false); parameters.push_back(psff);
- CommandParameter pgroup("group", "InputTypes", "", "", "groupOligos", "none", "none","sra",false,false); parameters.push_back(pgroup);
- CommandParameter poligos("oligos", "InputTypes", "", "", "groupOligos", "none", "none","sra",false,false); parameters.push_back(poligos);
- CommandParameter pfile("file", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","sra",false,false); parameters.push_back(pfile);
- CommandParameter pfastq("fastq", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","sra",false,false); parameters.push_back(pfastq);
+ CommandParameter psff("sff", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "oligos", "none", "none","",false,false,true); parameters.push_back(poligos);
+ CommandParameter pfile("file", "InputTypes", "", "", "sffFastQFile-oligos", "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("project", "InputTypes", "", "", "none", "none", "none","xml",false,true,true); parameters.push_back(pcontact);
+ CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
+ CommandParameter pmimark("mimark", "InputTypes", "", "", "none", "none", "none","xml",false,true,true); parameters.push_back(pmimark);
//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 pdatatype("datatype", "String", "METAGENOME", "", "", "", "","",false,false); parameters.push_back(pdatatype);
+ CommandParameter plibsource("libsource", "String", "METAGENOMIC", "", "", "", "","",false,false); parameters.push_back(plibsource);
+ CommandParameter plibselection("libselection", "String", "PCR", "", "", "", "","",false,false); parameters.push_back(plibselection);
+ CommandParameter porientation("orientation", "Multiple", "forward-reverse", "forward", "", "", "","",false,false); parameters.push_back(porientation);
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);
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, project, mimarksfile, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, checkorient, platform, orientation, libstrategy, datatype, 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 project parameter is used to provide your project file.\n";
+ helpString += "The oligos parameter is used to provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers, or you must provide a file option. \n";
+ helpString += "The mimark parameter is used to provide your mimarks file. You can create the template for this file using the get.mimarkspackage command.\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 new command should be in the following format: \n";
- helpString += "new(...)\n";
+ helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. The default is false.\n";
+ helpString += "The platform parameter is used to specify platform 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 orientation parameter is used to specify sequence orientation. Choices are: forward and reverse. Default=forward. 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 datatype parameter is used to specify datatype. Default=METAGENOME. Choices are METAGENOME,GENOME_SEQUENCING,METAGENOMIC_ASSEMBLY,ASSEMBLY,TRANSCRIPTOME,PROTEOMIC,MAP,CLONE_ENDS,TARGETED_LOCI,RANDOM_SURVEY,EXOME,VARIATION,EPIGENOMICS,PHENOTYPE,GENOTYPE,OTHER. This is a controlled vocabulary section in the XML file that will be generated. \n";
+ helpString += "sra(sff=sff=GHL4YHV01.sff, GHL4YHV01.oligos, project=test.project, mimark=MIMarksData.txt)\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);
+ inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
if (path == "") { parameters["file"] = inputDir + it->second; }
}
- it = parameters.find("group");
+ 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["group"] = inputDir + it->second; }
+ if (path == "") { parameters["oligos"] = inputDir + it->second; }
}
- it = parameters.find("oligos");
+ it = parameters.find("project");
//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["oligos"] = inputDir + it->second; }
+ if (path == "") { parameters["project"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("mimark");
+ //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["mimark"] = inputDir + it->second; }
}
}
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; }
+ if (oligosfile == "not found") { oligosfile = ""; }
+ else if(oligosfile == "not open") { abort = true; }
else { m->setOligosFile(oligosfile); }
+ contactfile = validParameter.validFile(parameters, "project", true);
+ if (contactfile == "not found") { contactfile = ""; m->mothurOut("[ERROR]: You must provide a project file before you can use the sra command."); m->mothurOutEndLine(); abort = true; }
+ else if(contactfile == "not open") { abort = true; }
+
+ mimarksfile = validParameter.validFile(parameters, "mimark", true);
+ if (mimarksfile == "not found") { mimarksfile = ""; m->mothurOut("[ERROR]: You must provide a mimark file before you can use the sra command. You can create a template for this file using the get.mimarkspackage command."); m->mothurOutEndLine(); abort = true; }
+ else if(mimarksfile == "not open") { abort = true; }
file = validParameter.validFile(parameters, "file", true);
if (file == "not open") { file = ""; abort = true; }
else if (file == "not found") { file = ""; }
- 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 ((file == "") && (oligosfile == "")) {
+ m->mothurOut("[ERROR]: You must provide an oligos file or file with oligos files in them 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 == "") && (file == "") && (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 ((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 _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
}
-
- //use only one Mutliple type
- platform = validParameter.validFile(parameters, "platform", false);
- if (platform == "not found") { platform = "454"; }
-
- if ((platform == "454") || (platform == "????") || (platform == "????") || (platform == "????")) { }
- else { m->mothurOut("Not a valid platform option. Valid platform options are 454, ...."); m->mothurOutEndLine(); abort = true; }
+ //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] = ' '; } }
+
+ dataType = validParameter.validFile(parameters, "datatype", false); if (dataType == "not found") { dataType = "METAGENOME"; }
+ if (!checkCasesDataType(dataType)) { abort = true; } //error message in function
+
+ //turn _ to spaces mothur's work around
+ for (int i = 0; i < dataType.length(); i++) { if (dataType[i] == '_') { dataType[i] = ' '; } }
+
+ orientation = validParameter.validFile(parameters, "orientation", false); if (orientation == "not found") { orientation = "forward"; }
+
+ if ((orientation == "forward") || (orientation == "reverse")) { }
+ else { m->mothurOut("[ERROR]: " + orientation + " is not a valid orientation option. Choices are: forward and reverse.\n"); m->mothurOutEndLine(); abort = true; }
+
string temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
m->mothurConvert(temp, bdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
-
+ checkorient = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; }
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ readContactFile();
+ readMIMarksFile();
+ if (oligosfile != "") { readOligos(); Groups.push_back("scrap"); }
+
+ if (m->control_pressed) { return 0; }
+
//parse files
- vector<string> filesBySample;
+ map<string, vector<string> > filesBySample;
+ isSFF = false;
if (file != "") { readFile(filesBySample); }
else if (sfffile != "") { parseSffFile(filesBySample); }
else if (fastqfile != "") { parseFastqFile(filesBySample); }
+ for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { Groups.push_back(*it); }
+
+ sanityCheckMiMarksGroups();
+
+ //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=\"" + centerName + "\">" + projectName + " </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>" + projectTitle + " </Title> \n";
+ out << "\t\t\t\t\t\t\t<Description><p>" + description + "</p></Description> \n";
+ if (website != "") {
+ 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</Descriptor>\n";
+ out << "\t\t\t\t\t\t<ProjectType>\n";
+ out << "\t\t\t\t\t\t\t<ProjectTypeSubmission sample_scope=\"eEnvironment\">\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";
+ 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\t\t<SPUID spuid_namespace=\"" + centerName + "\">" + projectName + " </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++) {
+
+ string barcodeForThisSample = Group2Barcode[Groups[i]][0];
+
+ 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=\"" + centerName + "\">" + Groups[i] + " </SPUID> \n";
+ out << "\t\t\t\t\t\t</SampleId>\n";
+ out << "\t\t\t\t\t\t<Organism>\n";
+ string organismName = "metagenome";
+ map<string, string>::iterator itOrganism = Group2Organism.find(Groups[i]);
+ if (itOrganism != Group2Organism.end()) { organismName = itOrganism->second; } //user supplied acceptable organism, so use it.
+ out << "\t\t\t\t\t\t\t<OrganismName>" + organismName + " </OrganismName> \n";
+ out << "\t\t\t\t\t\t</Organism>\n";
+ out << "\t\t\t\t\t\t<Package>" + packageType + "</Package>n";
+ out << "\t\t\t\t\t\t<Attributes>n";
+ //add biosample required attributes
+ map<string, map<string, string> >:: iterator it = mimarks.find(Groups[i]);
+ if (it != mimarks.end()) {
+ map<string, string> categories = it->second;
+ for (map<string, string>:: iterator it2 = categories.begin(); it2 != categories.end(); it2++) {
+ if (m->control_pressed) { break; }
+ out << "\t\t\t\t\t\t\t<Attribute attribute_name=\"" + it2->first + "\">\"" + it2->second + "\"</Attribute>\n";
+ }
+ }
+ 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";
+ out << "\t\t\t<Identifier>\n";
+ out << "\t\t\t\t<SPUID spuid_namespace=\"" + centerName + "\">" + Groups[i] + " </SPUID>\n";
+ out << "\t\t\t</Identifier>\n";
+ out << "\t\t</AddData>\n";
+ out << "\t</Action>\n";
+ }
+ //File objects
+ ////////////////////////////////////////////////////////
+ for (int i = 0; i < Groups.size(); i++) {
+
+ vector<string> thisGroupsFiles = filesBySample[Groups[i]];
+ string barcodeForThisSample = Group2Barcode[Groups[i]][0];
+
+ for (int j = 0; j < thisGroupsFiles.size(); j++) {
+ string libId = thisGroupsFiles[j] + "." + barcodeForThisSample;
+
+ 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]);
+ libId = pieces[0] + barcodeForThisSample;
+ out << "\t\t\t<File file_path=\"" + pieces[0] + "\">\n";
+ out << "\t\t\t\t<DataType>generic-data</DataType> \n";
+ out << "\t\t\t</File>\n";
+ vector<string> thisBarcodes; m->splitAtChar(Group2Barcode[Groups[i]][0], thisBarcodes, '.');
+ string forwardBarcode = thisBarcodes[0];
+ string reverseBarcode = thisBarcodes[1];
+ vector<string> thisPrimers; m->splitAtChar(Group2Primer[Groups[i]][0], thisPrimers, '.');
+ string forwardPrimer = thisPrimers[0];
+ string reversePrimer = thisPrimers[1];
+ //attributes
+ out << "\t\t\t<Attribute name=\"title\">" + mimarks[Groups[i]]["title"] + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"BarCode\">" + forwardBarcode + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"primer\">" + forwardPrimer + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"read_type\">forward</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_name\">" + libId + "</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";
+ out << "\t\t\t<Attribute name=\"instrument_model\">" + instrumentModel + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_construction_protocol\">" + mimarks[Groups[i]]["seq_methods"] + "</Attribute>\n";
+
+ out << "\t\t\t<File file_path=\"" + pieces[1] + "\">\n";
+ out << "\t\t\t\t<DataType>generic-data</DataType> \n";
+ out << "\t\t\t</File>\n";
+ out << "\t\t\t<Attribute name=\"title\">" + mimarks[Groups[i]]["title"] + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"BarCode\">" + reverseBarcode + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"primer\">" + reversePrimer + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"read_type\">reverse</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_name\">" + libId + "</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";
+ out << "\t\t\t<Attribute name=\"instrument_model\">" + instrumentModel + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_construction_protocol\">" + mimarks[Groups[i]]["seq_methods"] + "</Attribute>\n";
+
+ }else { //single
+ out << "\t\t\t<File file_path=\"" + thisGroupsFiles[j] + "\">\n";
+ out << "\t\t\t\t<DataType>generic-data</DataType> \n";
+ out << "\t\t\t</File>\n";
+ //attributes
+ out << "\t\t\t<Attribute name=\"title\">" + mimarks[Groups[i]]["title"] + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"BarCode\">" + Group2Barcode[Groups[i]][0] + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"primer\">" + Group2Primer[Groups[i]][0] + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"read_type\">" + orientation + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_name\">" + libId + "</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";
+ out << "\t\t\t<Attribute name=\"instrument_model\">" + instrumentModel + "</Attribute>\n";
+ out << "\t\t\t<Attribute name=\"library_construction_protocol\">" + mimarks[Groups[i]]["seq_methods"] + "</Attribute>\n";
+
+ }
+ ///////////////////bioProject info
+ out << "\t\t\t<AttributeRefId name=\"BioProject\">\n";
+ out << "\t\t\t\t<RefId>\n";
+ out << "\t\t\t\t\t<SPUID spuid_namespace=\"" + centerName + "\">" + projectName + " </SPUID> \n";
+ out << "\t\t\t\t</RefId>\n";
+ out << "\t\t\t</AttributeRefId>\n";
+ //////////////////bioSample info
+ out << "\t\t\t<AttributeRefId name=\"BioSample\">\n";
+ out << "\t\t\t\t<RefId>\n";
+ out << "\t\t\t\t\t<SPUID spuid_namespace=\"" + centerName + "\">" + Groups[i] + " </SPUID>\n";
+ out << "\t\t\t\t</RefId>\n";
+ out << "\t\t\t</AttributeRefId>\n";
+ //libID
+ out << "\t\t\t<Identifier>\n";
+ 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<LocalId>" + libId + " </LocalId>\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::readFile(vector<string>& files){
+int SRACommand::readContactFile(){
+ try {
+ lastName = ""; firstName = ""; submissionName = ""; email = ""; centerName = ""; centerType = ""; description = ""; website = ""; projectName = "";
+ projectTitle = ""; grantAgency = ""; grantId = ""; grantTitle = "";
+
+ 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; }
+ else if (key == "WEBSITE") { website = value; }
+ else if (key == "PROJECTNAME") { projectName = value; }
+ else if (key == "PROJECTTITLE") { projectTitle = value; }
+ else if (key == "GRANTID") { grantId = value; }
+ else if (key == "GRANTTITLE") { grantTitle = value; }
+ else if (key == "GRANTAGENCY") { grantAgency = value; }
+ }
+ in.close();
+
+ if (lastName == "") { m->mothurOut("[ERROR]: missing last name from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (firstName == "") { m->mothurOut("[ERROR]: missing first name from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (submissionName == "") { m->mothurOut("[ERROR]: missing submission name from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (email == "") { m->mothurOut("[ERROR]: missing email from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (centerName == "") { m->mothurOut("[ERROR]: missing center name from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (centerType == "") { m->mothurOut("[ERROR]: missing center type from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (description == "") { m->mothurOut("[ERROR]: missing description from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (projectTitle == "") { m->mothurOut("[ERROR]: missing project title from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (projectName == "") { m->mothurOut("[ERROR]: missing project name from project file, quitting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readContactFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//air, host_associated, human_associated, human_gut, human_oral, human_skin, human_vaginal, microbial, miscellaneous, plant_associated, sediment, soil, wastewater or water
+//all packages require: *sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon
+//air: *altitude
+//host_associated, human_associated, human_gut, human_oral, human_skin, human_vaginal, plant_associated: *host
+//microbial, sediment, soil: *depth *elev
+//water: *depth
+int SRACommand::readMIMarksFile(){
+ try {
+ //acceptable organisms
+ vector<string> acceptableOrganisms;
+ bool organismError = false;
+ //ecological
+ acceptableOrganisms.push_back("activated carbon metagenome"); acceptableOrganisms.push_back("activated sludge metagenome"); acceptableOrganisms.push_back("air metagenome"); acceptableOrganisms.push_back("anaerobic digester metagenome"); acceptableOrganisms.push_back("ant fungus garden metagenome"); acceptableOrganisms.push_back("aquatic metagenome"); acceptableOrganisms.push_back("activated carbon metagenome"); acceptableOrganisms.push_back("activated sludge metagenome"); acceptableOrganisms.push_back("beach sand metagenome"); acceptableOrganisms.push_back("biofilm metagenome"); acceptableOrganisms.push_back("biofilter metagenome"); acceptableOrganisms.push_back("biogas fermenter metagenome"); acceptableOrganisms.push_back("bioreactor metagenome"); acceptableOrganisms.push_back("bioreactor sludge metagenome"); acceptableOrganisms.push_back("clinical metagenome"); acceptableOrganisms.push_back("coal metagenome"); acceptableOrganisms.push_back("compost metagenome"); acceptableOrganisms.push_back("dust metagenome"); acceptableOrganisms.push_back("fermentation metagenome"); acceptableOrganisms.push_back("food fermentation metagenome"); acceptableOrganisms.push_back("food metagenome"); acceptableOrganisms.push_back("freshwater metagenome"); acceptableOrganisms.push_back("freshwater sediment metagenome"); acceptableOrganisms.push_back("groundwater metagenome"); acceptableOrganisms.push_back("halite metagenome"); acceptableOrganisms.push_back("hot springs metagenome"); acceptableOrganisms.push_back("hydrocarbon metagenome"); acceptableOrganisms.push_back("hydrothermal vent metagenome"); acceptableOrganisms.push_back("hypersaline lake metagenome"); acceptableOrganisms.push_back("ice metagenome"); acceptableOrganisms.push_back("indoor metagenome"); acceptableOrganisms.push_back("industrial waste metagenome"); acceptableOrganisms.push_back("mangrove metagenome"); acceptableOrganisms.push_back("marine metagenome"); acceptableOrganisms.push_back("marine sediment metagenome"); acceptableOrganisms.push_back("microbial mat metagenome"); acceptableOrganisms.push_back("mine drainage metagenome"); acceptableOrganisms.push_back("mixed culture metagenome"); acceptableOrganisms.push_back("oil production facility metagenome"); acceptableOrganisms.push_back("paper pulp metagenome"); acceptableOrganisms.push_back("permafrost metagenome"); acceptableOrganisms.push_back("plastisphere metagenome"); acceptableOrganisms.push_back("power plant metagenome"); acceptableOrganisms.push_back("retting rhizosphere metagenome"); acceptableOrganisms.push_back("rock metagenome"); acceptableOrganisms.push_back("salt lake metagenome"); acceptableOrganisms.push_back("saltern metagenome"); acceptableOrganisms.push_back("sediment metagenome"); acceptableOrganisms.push_back("snow metagenome"); acceptableOrganisms.push_back("soil metagenome"); acceptableOrganisms.push_back("stromatolite metagenome"); acceptableOrganisms.push_back("terrestrial metagenome"); acceptableOrganisms.push_back("tomb wall metagenome"); acceptableOrganisms.push_back("wastewater metagenome"); acceptableOrganisms.push_back("wetland metagenome"); acceptableOrganisms.push_back("whale fall metagenome");
+ //oganismal
+ acceptableOrganisms.push_back("algae metagenome"); acceptableOrganisms.push_back("ant metagenome"); acceptableOrganisms.push_back("bat metagenome"); acceptableOrganisms.push_back("beetle metagenome"); acceptableOrganisms.push_back("bovine gut metagenome"); acceptableOrganisms.push_back("bovine metagenome"); acceptableOrganisms.push_back("chicken gut metagenome"); acceptableOrganisms.push_back("coral metagenome"); acceptableOrganisms.push_back("echinoderm metagenome"); acceptableOrganisms.push_back("endophyte metagenome"); acceptableOrganisms.push_back("epibiont metagenome"); acceptableOrganisms.push_back("fish metagenome"); acceptableOrganisms.push_back("fossil metagenome"); acceptableOrganisms.push_back("gill metagenome"); acceptableOrganisms.push_back("gut metagenome"); acceptableOrganisms.push_back("honeybee metagenome"); acceptableOrganisms.push_back("human gut metagenome"); acceptableOrganisms.push_back("human lung metagenome"); acceptableOrganisms.push_back("human metagenome"); acceptableOrganisms.push_back("human nasal/pharyngeal metagenome"); acceptableOrganisms.push_back("human oral metagenome"); acceptableOrganisms.push_back("human skin metagenome"); acceptableOrganisms.push_back("insect gut metagenome"); acceptableOrganisms.push_back("insect metagenome"); acceptableOrganisms.push_back("mollusc metagenome"); acceptableOrganisms.push_back("mosquito metagenome"); acceptableOrganisms.push_back("mouse gut metagenome"); acceptableOrganisms.push_back("mouse metagenome"); acceptableOrganisms.push_back("mouse skin metagenome"); acceptableOrganisms.push_back("nematode metagenome"); acceptableOrganisms.push_back("oral metagenome"); acceptableOrganisms.push_back("phyllosphere metagenome"); acceptableOrganisms.push_back("pig metagenome"); acceptableOrganisms.push_back("plant metagenome"); acceptableOrganisms.push_back("primate metagenome"); acceptableOrganisms.push_back("rat metagenome"); acceptableOrganisms.push_back("root metagenome"); acceptableOrganisms.push_back("sea squirt metagenome"); acceptableOrganisms.push_back("seed metagenome"); acceptableOrganisms.push_back("shoot metagenome"); acceptableOrganisms.push_back("skin metagenome"); acceptableOrganisms.push_back("snake metagenome"); acceptableOrganisms.push_back("sponge metagenome"); acceptableOrganisms.push_back("stomach metagenome"); acceptableOrganisms.push_back("symbiont metagenome"); acceptableOrganisms.push_back("termite gut metagenome"); acceptableOrganisms.push_back("termite metagenome"); acceptableOrganisms.push_back("upper respiratory tract metagenome"); acceptableOrganisms.push_back("urine metagenome"); acceptableOrganisms.push_back("viral metagenome"); acceptableOrganisms.push_back("wallaby gut metagenome"); acceptableOrganisms.push_back("wasp metagenome"); acceptableOrganisms.push_back("sythetic metagenome"); acceptableOrganisms.push_back("metagenome");
+
+ vector<string> requiredFieldsForPackage;
+ requiredFieldsForPackage.push_back("sample_name"); requiredFieldsForPackage.push_back("organism");
+ requiredFieldsForPackage.push_back("collection_date"); requiredFieldsForPackage.push_back("biome");
+ requiredFieldsForPackage.push_back("feature"); requiredFieldsForPackage.push_back("material");
+ requiredFieldsForPackage.push_back("geo_loc_name"); requiredFieldsForPackage.push_back("lat_lon");
+ requiredFieldsForPackage.push_back("seq_methods"); requiredFieldsForPackage.push_back("title");
+ vector<string> chooseAtLeastOneForPackage;
+
+ ifstream in;
+ m->openInputFile(mimarksfile, in);
+
+ //read comments
+ string temp; packageType = "";
+ while(!in.eof()) {
+
+ if (m->control_pressed) { break; }
+ temp = m->getline(in); m->gobble(in);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + temp + "\n"); }
+
+ if (temp[0] == '#') {
+ int pos = temp.find("Environmental");
+ if (pos != string::npos) {
+ for (int i = pos+14; i < temp.length(); i++) {
+ if (!isspace(temp[i])) { packageType += temp[i]; }
+ else { i+= temp.length(); }
+ }
+ }
+ }
+ else{ break; } //hit headers line
+ }
+
+ vector<string> headers; m->splitAtChar(temp, headers, '\t');
+ m->removeBlanks(headers);
+ //remove * from required's
+ for (int i = 0; i < headers.size(); i++) {
+ if (headers[i][0] == '*') { headers[i] = headers[i].substr(1); }
+ if (headers[i][0] == '*') { headers[i] = headers[i].substr(1); chooseAtLeastOneForPackage.push_back(headers[i]); } //secondary condition
+ if (m->debug) { m->mothurOut("[DEBUG]: " + headers[i] + "\n"); }
+ }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: packageType = '" + packageType + "'\n"); }
+
+ //check to make sure package has all its required parts
+ //MIMARKS.specimen.water.3.0
+ if (packageType == "MIMARKS.specimen.air.3.0") { requiredFieldsForPackage.push_back("altitude"); }
+ else if ((packageType == "MIMARKS.specimen.host-associated.3.0") || (packageType == "MIMARKS.specimen.human-associated.3.0") || (packageType == "MIMARKS.specimen.human-gut.3.0") || (packageType == "MIMARKS.specimen.human-oral.3.0") || (packageType == "MIMARKS.specimen.human-skin.3.0") || (packageType == "MIMARKS.specimen.human-vaginal.3.0") || (packageType == "MIMARKS.specimen.plant-associated.3.0")) { requiredFieldsForPackage.push_back("host"); }
+ else if ((packageType == "MIMARKS.specimen.microbial.3.0") || (packageType == "MIMARKS.specimen.sediment.3.0") || (packageType == "soil")) { requiredFieldsForPackage.push_back("depth"); requiredFieldsForPackage.push_back("elev"); }
+ else if (packageType == "MIMARKS.specimen.water.3.0") { requiredFieldsForPackage.push_back("depth"); }
+ else if ((packageType == "MIMARKS.specimen.miscellaneous.3.0") || (packageType == "wastewater")) { }
+ else {
+ m->mothurOut("[ERROR]: unknown package " + packageType + ", please correct.\n"); m->control_pressed = true; in.close(); return 0;
+ }
+
+ if (!m->isSubset(headers, requiredFieldsForPackage)){
+ string requiredFields = "";
+ for (int i = 0; i < requiredFieldsForPackage.size()-1; i++) { requiredFields += requiredFieldsForPackage[i] + ", "; } requiredFields += requiredFieldsForPackage[requiredFieldsForPackage.size()-1];
+ m->mothurOut("[ERROR]: missing required fields for package, please correct. Required fields are " + requiredFields + ".\n"); m->control_pressed = true; in.close(); return 0;
+ }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: chooseAtLeastOneForPackage.size() = " + toString(chooseAtLeastOneForPackage.size()) + "\n"); }
+
+ if (!m->inUsersGroups(chooseAtLeastOneForPackage, headers)){ //returns true if any of the choose at least ones are in headers
+ string requiredFields = "";
+ for (int i = 0; i < chooseAtLeastOneForPackage.size()-1; i++) { requiredFields += chooseAtLeastOneForPackage[i] + ", "; cout << chooseAtLeastOneForPackage[i] << endl; }
+ if (chooseAtLeastOneForPackage.size() < 1) { requiredFields += chooseAtLeastOneForPackage[chooseAtLeastOneForPackage.size()-1]; }
+ m->mothurOut("[ERROR]: missing a choose at least one fields for the package, please correct. These are marked with '**'. Required fields are " + requiredFields + ".\n"); m->control_pressed = true; in.close(); return 0;
+ }
+
+ map<string, bool> allNA; for (int i = 1; i < headers.size(); i++) { allNA[headers[i]] = true; }
+ while(!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ temp = m->getline(in); m->gobble(in);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + temp + "\n"); }
+
+ string original = temp;
+ vector<string> linePieces; m->splitAtChar(temp, linePieces, '\t');
+ m->removeBlanks(linePieces);
+
+ if (linePieces.size() != headers.size()) { m->mothurOut("[ERROR]: line: " + original + " contains " + toString(linePieces.size()) + " columns, but you have " + toString(headers.size()) + " column headers, please correct.\n"); m->control_pressed = true; }
+ else {
+ map<string, map<string, string> >:: iterator it = mimarks.find(linePieces[0]);
+
+ if (it == mimarks.end()) {
+ map<string, string> categories;
+ //start after *sample_name
+ for (int i = 1; i < headers.size(); i++) {
+ categories[headers[i]] = linePieces[i];
+ //check the users inputs for appropriate organisms
+ if (headers[i] == "organism") {
+ if (!m->inUsersGroups(linePieces[i], acceptableOrganisms)) { //not an acceptable organism
+ organismError = true;
+ m->mothurOut("[WARNING]: " + linePieces[i]+ " is not an acceptable organism, changing to acceptable 'metagenome'. NCBI will allow you to modify the organism after submission.\n"); linePieces[i] = "metagenome"; categories[headers[i]] = linePieces[i];
+ }
+ Group2Organism[linePieces[0]] = linePieces[i];
+ }
+ if (linePieces[i] != "NA") { allNA[headers[i]] = false; }
+ }
+
+ //does this sample already match an existing sample?
+ bool isOkaySample = true;
+ for (map<string, map<string, string> >:: iterator it2 = mimarks.begin(); it2 != mimarks.end(); it2++) {
+ if (m->control_pressed) { break; }
+ bool allSame = true;
+ for (int i = 1; i < headers.size(); i++) {
+ if ((it2->second)[headers[i]] != categories[headers[i]]) { allSame = false; }
+ }
+ if (allSame) { m->mothurOut("[ERROR]: " + linePieces[0]+ " is a duplicate sample to " + it2->first + ". It has all the same attributes in the MIMarks file. Samples must have distinguishing features to be uploaded to the NCBI library, please correct.\n"); m->control_pressed = true; isOkaySample = false; }
+ }
+ if (isOkaySample) { mimarks[linePieces[0]] = categories; }
+ }else {
+ m->mothurOut("[ERROR]: " + linePieces[0]+ " is a duplicate sampleName. Sample names must be unique, please correct.\n"); m->control_pressed = true;
+ }
+ }
+ }
+ in.close();
+
+ //add in values for "scrap" group
+ map<string, string> categories;
+ //start after *sample_name
+ for (int i = 1; i < headers.size(); i++) {
+ categories[headers[i]] = "NA";
+ if (headers[i] == "organism") { categories[headers[i]] = "metagenome"; }
+ if (headers[i] == "seq_methods") { categories[headers[i]] = "these sequences were scrapped"; }
+ if (headers[i] == "title") { categories[headers[i]] = "these sequences were scrapped"; }
+ }
+ mimarks["scrap"] = categories;
+ Group2Organism["scrap"] = "metagenome";
+
+ if (organismError) {
+ string organismTypes = "";
+ for (int i = 0; i < acceptableOrganisms.size()-1; i++) { organismTypes += acceptableOrganisms[i] + ", "; }
+ organismTypes += acceptableOrganisms[acceptableOrganisms.size()-1];
+ m->mothurOut("\n[WARNING]: The acceptable organism choices are: " + organismTypes + ".\n\n\n");
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "readMIMarksFile");
+ 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"); }
+
+ if (inputDir != "") {
+ string path = m->hasPath(thisFileName1);
+ if (path == "") { thisFileName1 = inputDir + thisFileName1; }
+
+ path = m->hasPath(thisFileName2);
+ if (path == "") { thisFileName2 = inputDir + thisFileName2; }
+ }
+
+ //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(); }
+
+ int openReverse = 1;
+
+ ifstream in3;
+ 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 = thisFileName1.find(".sff");
+ if (pos != string::npos) {//these files are sff files
+ isSFF = true;
+ sfffile = thisFileName1; oligosfile = thisFileName2;
+ if (m->debug) { m->mothurOut("[DEBUG]: about to read oligos\n"); }
+ readOligos();
+ if (m->debug) { m->mothurOut("[DEBUG]: about to parse\n"); }
+ parseSffFile(files);
+ if (m->debug) { m->mothurOut("[DEBUG]: done parsing " + sfffile + "\n"); }
+ }else{
+ isSFF = false;
+ fastqfile = thisFileName1; oligosfile = thisFileName2;
+ if (m->debug) { m->mothurOut("[DEBUG]: about to read oligos\n"); }
+ readOligos();
+ if (m->debug) { m->mothurOut("[DEBUG]: about to parse\n"); }
+ parseFastqFile(files);
+ if (m->debug) { m->mothurOut("[DEBUG]: done parsing " + fastqfile + "\n"); }
+ }
+
+ }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;
}
}
}
//**********************************************************************************************************************
-int SRACommand::parseSffFile(vector<string>& files){
+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); }
- }
+
+ 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); }
+ if (m->isTrue(checkorient)) { commandString += ", checkorient=" + checkorient; }
+
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: sffinfo(" + commandString + ")"); m->mothurOutEndLine();
map<string, vector<string> > filenames = sffinfoCommand->getOutputFiles();
map<string, vector<string> >::iterator it = filenames.find("sff");
- if (it != filenames.end()) { files = it->second; }
+ 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) {
}
//**********************************************************************************************************************
-int SRACommand::parseFastqFile(vector<string>& files){
+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); }
- }
+
+ 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); }
+ if (m->isTrue(checkorient)) { commandString += ", checkorient=" + checkorient; }
+
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: fastq.info(" + commandString + ")"); m->mothurOutEndLine();
map<string, vector<string> > filenames = fastqinfoCommand->getOutputFiles();
map<string, vector<string> >::iterator it = filenames.find("fastq");
- if (it != filenames.end()) { files = it->second; }
+ 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) {
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 {
+ Oligos oligos(oligosfile);
+
+ if (m->control_pressed) { return false; } //error in reading oligos
+
+ if (oligos.hasPairedBarcodes()) { pairedOligos = true; }
+ else { pairedOligos = false; }
+
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ if (pairedOligos) {
+ map<int, oligosPair> barcodes = oligos.getPairedBarcodes();
+ map<int, oligosPair> primers = oligos.getPairedPrimers();
+ for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = oligos.getPrimerName(itPrimer->first);
+ string barcodeName = oligos.getBarcodeName(itBar->first);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
+ }
+ else{
+ comboGroupName = barcodeName + "." + primerName;
+ }
+ }
+ uniqueNames.insert(comboGroupName);
+
+ map<string, vector<string> >::iterator itGroup2Barcode = Group2Barcode.find(comboGroupName);
+ if (itGroup2Barcode == Group2Barcode.end()) {
+ vector<string> tempBarcodes; tempBarcodes.push_back((itBar->second).forward+"."+(itBar->second).reverse);
+ Group2Barcode[comboGroupName] = tempBarcodes;
+ }else {
+ Group2Barcode[comboGroupName].push_back((itBar->second).forward+"."+(itBar->second).reverse);
+ }
+
+ itGroup2Barcode = Group2Primer.find(comboGroupName);
+ if (itGroup2Barcode == Group2Primer.end()) {
+ vector<string> tempPrimers; tempPrimers.push_back((itPrimer->second).forward+"."+(itPrimer->second).reverse);
+ Group2Primer[comboGroupName] = tempPrimers;
+ }else {
+ Group2Primer[comboGroupName].push_back((itPrimer->second).forward+"."+(itPrimer->second).reverse);
+ }
+ }
+ }
+ }
+ }else {
+ map<string, int> barcodes = oligos.getBarcodes() ;
+ map<string, int> primers = oligos.getPrimers();
+ 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 = oligos.getPrimerName(itPrimer->second);
+ string barcodeName = oligos.getBarcodeName(itBar->second);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
+ }
+ else{
+ comboGroupName = barcodeName + "." + primerName;
+ }
+ }
+ uniqueNames.insert(comboGroupName);
+
+ map<string, vector<string> >::iterator itGroup2Barcode = Group2Barcode.find(comboGroupName);
+ if (itGroup2Barcode == Group2Barcode.end()) {
+ vector<string> tempBarcodes; tempBarcodes.push_back(itBar->first);
+ Group2Barcode[comboGroupName] = tempBarcodes;
+ }else {
+ Group2Barcode[comboGroupName].push_back(itBar->first);
+ }
+
+ itGroup2Barcode = Group2Primer.find(comboGroupName);
+ if (itGroup2Barcode == Group2Primer.end()) {
+ vector<string> tempPrimers; tempPrimers.push_back(itPrimer->first);
+ Group2Primer[comboGroupName] = tempPrimers;
+ }else {
+ Group2Primer[comboGroupName].push_back(itPrimer->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++; } }
+
+ 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);
+ }
+}
+//**********************************************************************************************************************
+//METAGENOME,GENOME_SEQUENCING,METAGENOMIC_ASSEMBLY,ASSEMBLY,TRANSCRIPTOME,PROTEOMIC,MAP,CLONE_ENDS,TARGETED_LOCI,RANDOM_SURVEY,EXOME,VARIATION,EPIGENOMICS,PHENOTYPE,GENOTYPE,OTHER
+bool SRACommand::checkCasesDataType(string& dataType){
+ try {
+ string original = dataType;
+ bool isOkay = true;
+
+ //remove users possible case errors
+ for (int i = 0; i < dataType.size(); i++) { dataType[i] = toupper(dataType[i]); }
+
+ if ((dataType == "METAGENOME") || (dataType == "GENOME_SEQUENCING") || (dataType == "METAGENOMIC_ASSEMBLY") || (dataType == "ASSEMBLY") || (dataType == "TRANSCRIPTOME") || (dataType == "PROTEOMIC") || (dataType == "MAP") || (dataType == "CLONE_ENDS") || (dataType == "TARGETED_LOCI") || (dataType == "RANDOM_SURVEY") || (dataType == "EXOME") || (dataType == "VARIATION") || (dataType == "EPIGENOMICS") || (dataType == "PHENOTYPE") || (dataType == "GENOTYPE") || (dataType == "OTHER")) { }
+ else { isOkay = false; }
+
+ if (isOkay) {
+
+ }else {
+ m->mothurOut("[ERROR]: " + original + " is not a valid datatype option. Valid datatype options are METAGENOME,GENOME_SEQUENCING,METAGENOMIC_ASSEMBLY,ASSEMBLY,TRANSCRIPTOME,PROTEOMIC,MAP,CLONE_ENDS,TARGETED_LOCI,RANDOM_SURVEY,EXOME,VARIATION,EPIGENOMICS,PHENOTYPE,GENOTYPE,OTHER."); m->mothurOutEndLine(); abort = true;
+ }
+
+ return isOkay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "checkCasesDataType");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+bool SRACommand::sanityCheckMiMarksGroups(){
+ try {
+ bool isOkay = true;
+
+ for (int i = 0; i < Groups.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ map<string, map<string, string> >::iterator it = mimarks.find(Groups[i]);
+ if (it == mimarks.end()) {
+ isOkay = false;
+ m->mothurOut("[ERROR]: MIMarks file is missing group " + Groups[i] + ", please correct.\n");
+ }
+ }
+
+ if (!isOkay) { m->control_pressed = true; }
+
+ return isOkay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "sanityCheckMiMarksGroups");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff