X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=b9436f8078df0da22408dafc889d16e62d8a7d6c;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=798ae64bfa88620fb6403f68842c50cee381ca25;hpb=1d7a10dc3dafd1606d6255bdb54e02429cbee47c;p=mothur.git diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index 798ae64..b9436f8 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -10,8 +10,56 @@ #include "filterseqscommand.h" #include "sequence.hpp" +//********************************************************************************************************************** +vector FilterSeqsCommand::getValidParameters(){ + try { + string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +FilterSeqsCommand::FilterSeqsCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["filter"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector FilterSeqsCommand::getRequiredParameters(){ + try { + string Array[] = {"fasta"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector FilterSeqsCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "getRequiredFiles"); + exit(1); + } +} /**************************************************************************************/ - FilterSeqsCommand::FilterSeqsCommand(string option) { try { abort = false; @@ -36,6 +84,11 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["filter"] = 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); if (inputDir == "not found"){ inputDir = ""; } @@ -80,10 +133,25 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { if (m->getDefaultPath() != "") { //default path is set string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]); m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = m->openInputFile(tryPath, in, "noerror"); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); fastafileNames[i] = tryPath; } } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]); + m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastafileNames[i] = tryPath; + } + } + in.close(); if (ableToOpen == 1) { @@ -147,13 +215,14 @@ void FilterSeqsCommand::help(){ try { m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n"); - m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n"); + m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n"); m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n"); m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n"); m->mothurOut("The trump parameter .... The default is ...\n"); m->mothurOut("The soft parameter .... The default is ....\n"); m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n"); m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n"); + m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); m->mothurOut("The filter.seqs command should be in the following format: \n"); m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n"); m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n"); @@ -187,7 +256,7 @@ int FilterSeqsCommand::execute() { m->mothurOutEndLine(); m->mothurOutEndLine(); - if (m->control_pressed) { return 0; } + if (m->control_pressed) { outputTypes.clear(); return 0; } #ifdef USE_MPI int pid; @@ -206,7 +275,7 @@ int FilterSeqsCommand::execute() { m->openOutputFile(filterFile, outFilter); outFilter << filter << endl; outFilter.close(); - outputNames.push_back(filterFile); + outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile); #ifdef USE_MPI } @@ -225,7 +294,7 @@ int FilterSeqsCommand::execute() { if(filter[i] == '1'){ filteredLength++; } } - if (m->control_pressed) { for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } m->mothurOutEndLine(); @@ -309,8 +378,8 @@ int FilterSeqsCommand::filterSequences() { //wait on chidren for(int i = 1; i < processors; i++) { - char buf[4]; - MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); + char buf[5]; + MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); } }else { //you are a child process @@ -330,11 +399,11 @@ int FilterSeqsCommand::filterSequences() { if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } - char buf[4]; + char buf[5]; strcpy(buf, "done"); //tell parent you are done. - MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } MPI_File_close(&outMPI); @@ -372,7 +441,7 @@ int FilterSeqsCommand::filterSequences() { if (m->control_pressed) { return 1; } #endif #endif - outputNames.push_back(filteredFasta); + outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta); } return 0; @@ -541,7 +610,11 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) { out.close(); exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } } //force parent to wait until all the processes are done @@ -905,7 +978,11 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) out.close(); exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } } //parent do your part