X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=1aa133f38c379fd40c495d2c2a844de292c17f51;hb=d945488119ad368b180537f36ed40298ff170f39;hp=5c890404dea8ed4c5e9c6dae0cef4f41a1ef5f70;hpb=48335c6b6ecee614c30d22751c2880953c20e2f4;p=mothur.git diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp index 5c89040..1aa133f 100644 --- a/pairwiseseqscommand.cpp +++ b/pairwiseseqscommand.cpp @@ -23,44 +23,66 @@ //********************************************************************************************************************** -vector PairwiseSeqsCommand::getValidParameters(){ +vector PairwiseSeqsCommand::setParameters(){ try { - string AlignArray[] = {"fasta","align","match","mismatch","gapopen","gapextend", "processors","calc","compress","cutoff","countends","output","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); + CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign); + CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch); + CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch); + CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen); + CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput); + CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc); + CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends); + CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress); + CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "PairwiseSeqsCommand", "getValidParameters"); + m->errorOut(e, "PairwiseSeqsCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector PairwiseSeqsCommand::getRequiredParameters(){ +string PairwiseSeqsCommand::getHelpString(){ try { - string AlignArray[] = {"fasta"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); - return myArray; + string helpString = ""; + helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n"; + helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n"; + helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"; + helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n"; + helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"; + helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"; + helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"; + helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"; + helpString += "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n"; + helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n"; + helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n"; + helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n"; + helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n"; + helpString += "The pairwise.seqs command should be in the following format: \n"; + helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n"; + helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "PairwiseSeqsCommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector PairwiseSeqsCommand::getRequiredFiles(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PairwiseSeqsCommand", "getRequiredFiles"); + m->errorOut(e, "PairwiseSeqsCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** PairwiseSeqsCommand::PairwiseSeqsCommand(){ try { abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["phylip"] = tempOutNames; outputTypes["column"] = tempOutNames; @@ -79,10 +101,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { if(option == "help") { help(); abort = true; calledHelp = true; } else { - - //valid paramters for this command - string AlignArray[] = {"fasta","align","match","mismatch","gapopen","gapextend", "processors","cutoff","compress","calc","countends","output","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -110,55 +129,75 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { if (inputDir == "not found"){ inputDir = ""; } fastaFileName = validParameter.validFile(parameters, "fasta", false); - if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the pairwise.seqs command."); m->mothurOutEndLine(); abort = true; } + if (fastaFileName == "not found") { + //if there is a current fasta file, use it + string filename = m->getFastaFile(); + if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + } else { m->splitAtDash(fastaFileName, fastaFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < fastaFileNames.size(); i++) { - if (inputDir != "") { - string path = m->hasPath(fastaFileNames[i]); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } - } - - int ableToOpen; - ifstream in; - - ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); - - //if you can't open it, try default location - if (ableToOpen == 1) { - 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(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - fastaFileNames[i] = tryPath; + bool ignore = false; + if (fastaFileNames[i] == "current") { + fastaFileNames[i] = m->getFastaFile(); + if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; } } - //if you can't open it, try output 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; + if (!ignore) { + + if (inputDir != "") { + string path = m->hasPath(fastaFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } } - } + + int ableToOpen; + ifstream in; + + ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); - in.close(); + //if you can't open it, try default location + if (ableToOpen == 1) { + 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(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + //if you can't open it, try output 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) { - m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - fastaFileNames.erase(fastaFileNames.begin()+i); - i--; + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; + } } } @@ -181,8 +220,9 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; } convert(temp, gapExtend); - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } - convert(temp, processors); + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + convert(temp, processors); temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; } convert(temp, cutoff); @@ -231,37 +271,6 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option) { exit(1); } } -//********************************************************************************************************************** -PairwiseSeqsCommand::~PairwiseSeqsCommand(){} -//********************************************************************************************************************** - -void PairwiseSeqsCommand::help(){ - try { - m->mothurOut("The pairwise.seqs command reads a fasta file and creates distance matrix.\n"); - m->mothurOut("The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n"); - m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); - m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n"); - m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"); - m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"); - m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"); - m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"); - m->mothurOut("The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n"); - m->mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n"); - m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n"); - m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n"); - m->mothurOut("The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n"); - m->mothurOut("The pairwise.seqs command should be in the following format: \n"); - m->mothurOut("pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n"); - m->mothurOut("Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "PairwiseSeqsCommand", "help"); - exit(1); - } -} - - //********************************************************************************************************************** int PairwiseSeqsCommand::execute(){