X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=772113baf83e9fbbd057794103f46ffa21c21fda;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=d24d2cae51d0610af4a9fb5517c676058a7a4af6;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp index d24d2ca..772113b 100644 --- a/clusterfragmentscommand.cpp +++ b/clusterfragmentscommand.cpp @@ -8,6 +8,7 @@ */ #include "clusterfragmentscommand.h" +#include "needlemanoverlap.hpp" //********************************************************************************************************************** //sort by unaligned @@ -25,66 +26,71 @@ inline bool comparePriority(seqRNode first, seqRNode second) { return better; } //********************************************************************************************************************** -vector ClusterFragmentsCommand::getValidParameters(){ +vector ClusterFragmentsCommand::setParameters(){ try { - string AlignArray[] = {"fasta","name","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs); + CommandParameter ppercent("percent", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppercent); + 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, "ClusterFragmentsCommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -ClusterFragmentsCommand::ClusterFragmentsCommand(){ - try { - abort = true; - //initialize outputTypes - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["name"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "ClusterFragmentsCommand", "ClusterFragmentsCommand"); + m->errorOut(e, "ClusterFragmentsCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector ClusterFragmentsCommand::getRequiredParameters(){ +string ClusterFragmentsCommand::getHelpString(){ try { - string Array[] = {"fasta"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + string helpString = ""; + helpString += "The cluster.fragments command groups sequences that are part of a larger sequence.\n"; + helpString += "The cluster.fragments command outputs a new fasta and name file.\n"; + helpString += "The cluster.fragments command parameters are fasta, name, diffs and percent. The fasta parameter is required, unless you have a valid current file. \n"; + helpString += "The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n"; + helpString += "The diffs parameter allows you to set the number of differences allowed, default=0. \n"; + helpString += "The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster.\n"; + helpString += "You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge. \n"; + helpString += "The cluster.fragments command should be in the following format: \n"; + helpString += "cluster.fragments(fasta=yourFastaFile, names=yourNamesFile) \n"; + helpString += "Example cluster.fragments(fasta=amazon.fasta).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "ClusterFragmentsCommand", "getRequiredParameters"); + m->errorOut(e, "ClusterFragmentsCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector ClusterFragmentsCommand::getRequiredFiles(){ +ClusterFragmentsCommand::ClusterFragmentsCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "ClusterFragmentsCommand", "getRequiredFiles"); + m->errorOut(e, "ClusterFragmentsCommand", "ClusterFragmentsCommand"); exit(1); } } //********************************************************************************************************************** ClusterFragmentsCommand::ClusterFragmentsCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"fasta","name","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -126,8 +132,13 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) { //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the cluster.fragments command."); m->mothurOutEndLine(); abort = true; } - else if (fastafile == "not open") { abort = true; } + if (fastafile == "not found") { + fastafile = m->getFastaFile(); + if (fastafile != "") { m->mothurOut("Using " + fastafile + " 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 if (fastafile == "not open") { fastafile = ""; abort = true; } + else { m->setFastaFile(fastafile); } //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); } @@ -136,8 +147,21 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) { // ...at some point should added some additional type checking... namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not found") { namefile = ""; } - else if (namefile == "not open") { abort = true; } - else { readNameFile(); } + else if (namefile == "not open") { namefile = ""; abort = true; } + else { readNameFile(); m->setNameFile(namefile); } + + string temp; + temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found"){ temp = "0"; } + m->mothurConvert(temp, diffs); + + temp = validParameter.validFile(parameters, "percent", false); if (temp == "not found"){ temp = "0"; } + m->mothurConvert(temp, percent); + + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } } @@ -146,31 +170,11 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) { exit(1); } } - -//********************************************************************************************************************** -ClusterFragmentsCommand::~ClusterFragmentsCommand(){} -//********************************************************************************************************************** -void ClusterFragmentsCommand::help(){ - try { - m->mothurOut("The cluster.fragments command groups sequences that are part of a larger sequence.\n"); - m->mothurOut("The cluster.fragments command outputs a new fasta and name file.\n"); - m->mothurOut("The cluster.fragments command parameters are fasta and name. The fasta parameter is required. \n"); - m->mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n"); - m->mothurOut("The cluster.fragments command should be in the following format: \n"); - m->mothurOut("cluster.fragments(fasta=yourFastaFile, names=yourNamesFile) \n"); - m->mothurOut("Example cluster.fragments(fasta=amazon.fasta).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "ClusterFragmentsCommand", "help"); - exit(1); - } -} //********************************************************************************************************************** int ClusterFragmentsCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } int start = time(NULL); @@ -201,10 +205,8 @@ int ClusterFragmentsCommand::execute(){ if (alignSeqs[j].active) { //this sequence has not been merged yet string jBases = alignSeqs[j].seq.getUnaligned(); - - int pos = iBases.find(jBases); - - if (pos != string::npos) { + + if (isFragment(iBases, jBases)) { //merge alignSeqs[i].names += ',' + alignSeqs[j].names; alignSeqs[i].numIdentical += alignSeqs[j].numIdentical; @@ -229,7 +231,7 @@ int ClusterFragmentsCommand::execute(){ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile)); string newFastaFile = fileroot + "fragclust.fasta"; - string newNamesFile = fileroot + "names"; + string newNamesFile = fileroot + "fragclust.names"; if (m->control_pressed) { return 0; } @@ -241,7 +243,7 @@ int ClusterFragmentsCommand::execute(){ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); - if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; } + if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -249,6 +251,18 @@ int ClusterFragmentsCommand::execute(){ m->mothurOut(newNamesFile); m->mothurOutEndLine(); outputNames.push_back(newFastaFile); outputNames.push_back(newNamesFile); outputTypes["fasta"].push_back(newFastaFile); outputTypes["name"].push_back(newNamesFile); m->mothurOutEndLine(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + itTypes = outputTypes.find("name"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } + } return 0; @@ -258,7 +272,63 @@ int ClusterFragmentsCommand::execute(){ exit(1); } } - +//*************************************************************************************************************** +bool ClusterFragmentsCommand::isFragment(string seq1, string seq2){ + try { + bool fragment = false; + + //exact match + int pos = seq1.find(seq2); + if (pos != string::npos) { return true; } + //no match, no diffs wanted + else if ((diffs == 0) && (percent == 0)) { return false; } + else { //try aligning and see if you can find it + + //find number of acceptable differences for this sequence fragment + int totalDiffs; + if (diffs == 0) { //you didnt set diffs you want a percentage + totalDiffs = floor((seq2.length() * (percent / 100.0))); + }else if (percent == 0) { //you didn't set percent you want diffs + totalDiffs = diffs; + }else if ((percent != 0) && (diffs != 0)) { //you want both, set total diffs to smaller of 2 + totalDiffs = diffs; + int percentDiff = floor((seq2.length() * (percent / 100.0))); + if (percentDiff < totalDiffs) { totalDiffs = percentDiff; } + } + + Alignment* alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (seq1.length()+totalDiffs+1)); + + //use needleman to align + alignment->align(seq2, seq1); + string tempSeq2 = alignment->getSeqAAln(); + string temp = alignment->getSeqBAln(); + + delete alignment; + + //chop gap ends + int startPos = 0; + int endPos = tempSeq2.length()-1; + for (int i = 0; i < tempSeq2.length(); i++) { if (isalpha(tempSeq2[i])) { startPos = i; break; } } + for (int i = tempSeq2.length()-1; i >= 0; i--) { if (isalpha(tempSeq2[i])) { endPos = i; break; } } + + //count number of diffs + int numDiffs = 0; + for (int i = startPos; i <= endPos; i++) { + if (tempSeq2[i] != temp[i]) { numDiffs++; } + } + + if (numDiffs <= totalDiffs) { fragment = true; } + + } + + return fragment; + + } + catch(exception& e) { + m->errorOut(e, "ClusterFragmentsCommand", "isFragment"); + exit(1); + } +} /**************************************************************************************************/ int ClusterFragmentsCommand::readFASTA(){ try {