X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=68450fb15a7b140803aab2d54d8c5bc84e7ce688;hb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;hp=e024a242ed8b35771580b00cffd66bc7dd78d66d;hpb=986663e2220f6b043ee83d1699cfa081dc49cbed;p=mothur.git diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index e024a24..68450fb 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -8,146 +8,150 @@ */ #include "filterseqscommand.h" +#include "sequence.hpp" /**************************************************************************************/ -FilterSeqsCommand::FilterSeqsCommand(){ - - globaldata = GlobalData::getInstance(); - - if(globaldata->getFastaFile() == "") { cout << "You must enter a fasta formatted file" << endl; } - trump = globaldata->getTrump()[0]; - numSeqs = 0; - -} - -/**************************************************************************************/ - -void FilterSeqsCommand::doHard() { - - string hardName = globaldata->getHard(); - string hardFilter = ""; +FilterSeqsCommand::FilterSeqsCommand(string option){ + try { + abort = false; - ifstream fileHandle; - openInputFile(hardName, fileHandle); - - fileHandle >> filter; - -} - -/**************************************************************************************/ - -void FilterSeqsCommand::doTrump(Sequence seq) { - - string curAligned = seq.getAligned(); - - for(int j = 0; j < alignmentLength; j++) { - if(curAligned[j] == trump){ - filter[j] = '0'; + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"fasta", "trump", "soft", "hard", "vertical"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //check for required parameters + fastafile = validParameter.validFile(parameters, "fasta", true); + if (fastafile == "not found") { mothurOut("fasta is a required parameter for the filter.seqs command."); mothurOutEndLine(); abort = true; } + else if (fastafile == "not open") { abort = true; } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + + string temp; + temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; } + trump = temp[0]; + + temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; } + else { soft = (float)atoi(temp.c_str()) / 100.0; } + + hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; } + else if (hard == "not open") { abort = true; } + + vertical = validParameter.validFile(parameters, "vertical", false); if (vertical == "not found") { vertical = "T"; } + + numSeqs = 0; + + if (abort == false) { + + if (soft != 0) { F.setSoft(soft); } + if (trump != '*') { F.setTrump(trump); } + + } + } + } - -} - -/**************************************************************************************/ - -void FilterSeqsCommand::doVertical() { - - for(int i=0;i= threshold) { keep = 1; } - else if(t[i] >= threshold) { keep = 1; } - else if(g[i] >= threshold) { keep = 1; } - else if(c[i] >= threshold) { keep = 1; } +void FilterSeqsCommand::help(){ + try { + mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n"); + mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n"); + mothurOut("The fasta parameter is required.\n"); + mothurOut("The trump parameter .... The default is ...\n"); + mothurOut("The soft parameter .... The default is ....\n"); + mothurOut("The hard parameter .... The default is ....\n"); + mothurOut("The vertical parameter .... The default is T.\n"); + mothurOut("The filter.seqs command should be in the following format: \n"); + mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n"); + mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n"); + mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); - if(keep == 0) { filter[i] = 0; } } -} - -/**************************************************************************************/ - -void FilterSeqsCommand::getFreqs(Sequence seq) { - - string curAligned = seq.getAligned();; - - for(int j=0;jgetFastaFile(), inFASTA); + openInputFile(fastafile, inFASTA); Sequence testSeq(inFASTA); alignmentLength = testSeq.getAlignLength(); inFASTA.seekg(0); - if(globaldata->getSoft() != "" || isTrue(globaldata->getVertical())){ - a.assign(alignmentLength, 0); - t.assign(alignmentLength, 0); - g.assign(alignmentLength, 0); - c.assign(alignmentLength, 0); - gap.assign(alignmentLength, 0); - } - if(globaldata->getSoft() != ""){ - soft = (float)atoi(globaldata->getSoft().c_str()) / 100.0; + F.setLength(alignmentLength); + + if(soft != 0 || isTrue(vertical)){ + F.initialize(); } - if(globaldata->getHard().compare("") != 0) { doHard(); } - else { filter = string(alignmentLength, '1'); } + if(hard.compare("") != 0) { F.doHard(hard); } + else { F.setFilter(string(alignmentLength, '1')); } - if(globaldata->getTrump().compare("") != 0 || isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ - - while(!inFASTA.eof()){ + if(trump != '*' || isTrue(vertical) || soft != 0){ + while(!inFASTA.eof()){ //read through and create the filter... Sequence seq(inFASTA); - if(globaldata->getTrump().compare("") != 0) { doTrump(seq); } - if(isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ getFreqs(seq); } + if(trump != '*'){ F.doTrump(seq); } + if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); } numSeqs++; cout.flush(); } } inFASTA.close(); + F.setNumSeqs(numSeqs); + - if(isTrue(globaldata->getVertical()) == 1) { doVertical(); } - if(globaldata->getSoft().compare("") != 0) { doSoft(); } + if(isTrue(vertical) == 1) { F.doVertical(); } + if(soft != 0) { F.doSoft(); } + + filter = F.getFilter(); ofstream outFilter; - string filterFile = getRootName(globaldata->inputFileName) + "filter"; + string filterFile = getRootName(fastafile) + "filter"; openOutputFile(filterFile, outFilter); outFilter << filter << endl; outFilter.close(); - - openInputFile(globaldata->getFastaFile(), inFASTA); - string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta"; + ifstream inFasta2; + openInputFile(fastafile, inFasta2); + string filteredFasta = getRootName(fastafile) + "filter.fasta"; ofstream outFASTA; openOutputFile(filteredFasta, outFASTA); numSeqs = 0; - while(!inFASTA.eof()){ - Sequence seq(inFASTA); + while(!inFasta2.eof()){ + Sequence seq(inFasta2); string align = seq.getAligned(); string filterSeq = ""; @@ -159,10 +163,10 @@ int FilterSeqsCommand::execute() { outFASTA << '>' << seq.getName() << endl << filterSeq << endl; numSeqs++; - gobble(inFASTA); + gobble(inFasta2); } outFASTA.close(); - inFASTA.close(); + inFasta2.close(); int filteredLength = 0; @@ -170,23 +174,17 @@ int FilterSeqsCommand::execute() { if(filter[i] == '1'){ filteredLength++; } } - cout << endl; - cout << "Length of filtered alignment: " << filteredLength << endl; - cout << "Number of columns removed: " << alignmentLength-filteredLength << endl; - cout << "Length of the original alignment: " << alignmentLength << endl; - cout << "Number of sequences used to construct filter: " << numSeqs << endl; - - globaldata->clear(); + mothurOutEndLine(); + mothurOut("Length of filtered alignment: " + toString(filteredLength)); mothurOutEndLine(); + mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); mothurOutEndLine(); + mothurOut("Length of the original alignment: " + toString(alignmentLength)); mothurOutEndLine(); + mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); mothurOutEndLine(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "FilterSeqsCommand", "execute"); exit(1); } }