X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=38378491c072c1ed33cc257ec954de6a81f3bb7d;hb=cd9dbd8b53bbe32af3e9c6bead4aa6d796a278a5;hp=a38bf8f34ad0e15e98e85f5b4ad627babefcbf2b;hpb=6f4b9401f7deb8aaf0d87659298308f4138cc3b0;p=mothur.git diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp index a38bf8f..3837849 100644 --- a/classifyseqscommand.cpp +++ b/classifyseqscommand.cpp @@ -11,6 +11,7 @@ #include "sequence.hpp" #include "bayesian.h" #include "phylotree.h" +#include "phylosummary.h" #include "knn.h" //********************************************************************************************************************** @@ -25,7 +26,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { else { //valid paramters for this command - string AlignArray[] = {"template","fasta","name","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"}; + string AlignArray[] = {"template","fasta","name","group","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); OptionParser parser(option); @@ -62,6 +63,14 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["taxonomy"] = inputDir + it->second; } } + + it = parameters.find("group"); + //user has given a template file + if(it != parameters.end()){ + path = hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["group"] = inputDir + it->second; } + } } //check for required parameters @@ -73,6 +82,10 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { } else if (templateFileName == "not open") { abort = true; } + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + fastaFileName = validParameter.validFile(parameters, "fasta", false); if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true; } else { @@ -250,6 +263,7 @@ void ClassifySeqsCommand::help(){ m->mothurOut("The template, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is kmer.\n"); m->mothurOut("The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n"); + m->mothurOut("The group parameter allows you add a group file so you can have the summary totals broken up by group.\n"); m->mothurOut("The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n"); m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n"); m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); @@ -491,50 +505,40 @@ int ClassifySeqsCommand::execute(){ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); start = time(NULL); - //make taxonomy tree from new taxonomy file - PhyloTree taxaBrowser; + PhyloSummary taxaSum(taxonomyFileName, groupfile); if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } - ifstream in; - openInputFile(tempTaxonomyFile, in); - - //read in users taxonomy file and add sequences to tree - string name, taxon; - while(!in.eof()){ - in >> name >> taxon; gobble(in); - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(tempTaxonomyFile.c_str()); delete classify; return 0; } + if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); } + else { + ifstream in; + openInputFile(tempTaxonomyFile, in); - if (namefile != "") { + //read in users taxonomy file and add sequences to tree + string name, taxon; + while(!in.eof()){ + in >> name >> taxon; gobble(in); + itNames = nameMap.find(name); if (itNames == nameMap.end()) { m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1); }else{ for (int i = 0; i < itNames->second; i++) { - taxaBrowser.addSeqToTree(name+toString(i), taxon); //add it as many times as there are identical seqs + taxaSum.addSeqToTree(name+toString(i), taxon); //add it as many times as there are identical seqs } } - }else { taxaBrowser.addSeqToTree(name, taxon); } //add it once + } + in.close(); } - in.close(); - - taxaBrowser.assignHeirarchyIDs(0); - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(tempTaxonomyFile.c_str()); delete classify; return 0; } - - taxaBrowser.binUnclassified(); - remove(tempTaxonomyFile.c_str()); if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } - //print summary file ofstream outTaxTree; openOutputFile(taxSummary, outTaxTree); - taxaBrowser.print(outTaxTree); + taxaSum.print(outTaxTree); outTaxTree.close(); //output taxonomy with the unclassified bins added @@ -546,9 +550,10 @@ int ClassifySeqsCommand::execute(){ openOutputFile(unclass, outTax); //get maxLevel from phylotree so you know how many 'unclassified's to add - int maxLevel = taxaBrowser.getMaxLevel(); + int maxLevel = taxaSum.getMaxLevel(); //read taxfile - this reading and rewriting is done to preserve the confidence scores. + string name, taxon; while (!inTax.eof()) { if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; } @@ -564,6 +569,9 @@ int ClassifySeqsCommand::execute(){ remove(newTaxonomyFile.c_str()); rename(unclass.c_str(), newTaxonomyFile.c_str()); + m->mothurOutEndLine(); + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); + #ifdef USE_MPI } #endif @@ -572,10 +580,7 @@ int ClassifySeqsCommand::execute(){ m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); - - //m->mothurOutEndLine(); - //m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); } delete classify;