X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=115e930969323ba4655e0b5ba5c2a8e1166a1397;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=8ae76d9836c31b0d3a37ac41d58a6aa54db6e859;hpb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;p=mothur.git diff --git a/shhhercommand.cpp b/shhhercommand.cpp index 8ae76d9..115e930 100644 --- a/shhhercommand.cpp +++ b/shhhercommand.cpp @@ -47,6 +47,30 @@ string ShhherCommand::getHelpString(){ } } //********************************************************************************************************************** +string ShhherCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "fasta") { outputFileName = "shhh.fasta"; } + else if (type == "name") { outputFileName = "shhh.names"; } + else if (type == "group") { outputFileName = "shhh.groups"; } + else if (type == "counts") { outputFileName = "shhh.counts"; } + else if (type == "qfile") { outputFileName = "shhh.qual"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ShhherCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** ShhherCommand::ShhherCommand(){ try { @@ -54,8 +78,12 @@ ShhherCommand::ShhherCommand(){ setParameters(); //initialize outputTypes -// vector tempOutNames; -// outputTypes["pn.dist"] = tempOutNames; + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["counts"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; } catch(exception& e) { @@ -96,9 +124,13 @@ ShhherCommand::ShhherCommand(string option) { } //initialize outputTypes - vector tempOutNames; -// outputTypes["pn.dist"] = tempOutNames; - // outputTypes["fasta"] = tempOutNames; + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["counts"] = tempOutNames; + outputTypes["qfile"] = 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); @@ -770,7 +802,7 @@ string ShhherCommand::createNamesFile(){ duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ','; } - string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names"; + string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName) + getOutputFileNameTag("name"); ofstream nameFile; m->openOutputFile(nameFileName, nameFile); @@ -1614,7 +1646,7 @@ void ShhherCommand::writeQualities(vector otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.qual"; + string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile"); ofstream qualityFile; m->openOutputFile(qualityFileName, qualityFile); @@ -1721,7 +1753,7 @@ void ShhherCommand::writeSequences(vector otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.fasta"; + string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta"); ofstream fastaFile; m->openOutputFile(fastaFileName, fastaFile); @@ -1769,7 +1801,7 @@ void ShhherCommand::writeNames(vector otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.names"; + string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name"); ofstream nameFile; m->openOutputFile(nameFileName, nameFile); @@ -1807,14 +1839,17 @@ void ShhherCommand::writeGroups(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); - string groupFileName = fileRoot + "shhh.groups"; + string fileRoot = m->getRootName(m->getSimpleName(flowFileName)); + int pos = fileRoot.find_first_of('.'); + string fileGroup = fileRoot; + if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); } + string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group"); ofstream groupFile; m->openOutputFile(groupFileName, groupFile); for(int i=0;icontrol_pressed) { break; } - groupFile << seqNameVector[i] << '\t' << fileRoot << endl; + groupFile << seqNameVector[i] << '\t' << fileGroup << endl; } groupFile.close(); outputNames.push_back(groupFileName); @@ -1832,7 +1867,7 @@ void ShhherCommand::writeClusters(vector otuCounts){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); } - string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.counts"; + string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) +getOutputFileNameTag("counts"); ofstream otuCountsFile; m->openOutputFile(otuCountsFileName, otuCountsFile); @@ -2283,31 +2318,34 @@ int ShhherCommand::driver(vector filenames, string thisCompositeFASTAFil if ((large) && (g == 0)) { flowFileName = filenames[i]; theseFlowFileNames[0] = filenames[i]; } string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir = m->hasPath(flowFileName); } - string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.qual"; - string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.fasta"; - string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.names"; - string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.counts"; - string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)); - string groupFileName = fileRoot + "shhh.groups"; + string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile"); + string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta"); + string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name"); + string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("counts"); + string fileRoot = m->getRootName(m->getSimpleName(flowFileName)); + int pos = fileRoot.find_first_of('.'); + string fileGroup = fileRoot; + if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); } + string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group"); writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; } writeSequences(thisCompositeFASTAFileName, numOTUs, numFlowCells, fastaFileName, otuCounts, uniqueFlowgrams, seqNameVector, aaI, centroids);if (m->control_pressed) { break; } writeNames(thisCompositeNamesFileName, numOTUs, nameFileName, otuCounts, seqNameVector, aaI, nSeqsPerOTU); if (m->control_pressed) { break; } writeClusters(otuCountsFileName, numOTUs, numFlowCells,otuCounts, centroids, uniqueFlowgrams, seqNameVector, aaI, nSeqsPerOTU, lengths, flowDataIntI); if (m->control_pressed) { break; } - writeGroups(groupFileName, fileRoot, numSeqs, seqNameVector); if (m->control_pressed) { break; } + writeGroups(groupFileName, fileGroup, numSeqs, seqNameVector); if (m->control_pressed) { break; } if (large) { if (g > 0) { - m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.qual")); + m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("qfile"))); m->mothurRemove(qualityFileName); - m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.fasta")); + m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("fasta"))); m->mothurRemove(fastaFileName); - m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.names")); + m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("name"))); m->mothurRemove(nameFileName); - m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.counts")); + m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("counts"))); m->mothurRemove(otuCountsFileName); - m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.groups")); + m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("group"))); m->mothurRemove(groupFileName); } m->mothurRemove(theseFlowFileNames[g]);