X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=5af8e959a6caa3edd98a33a21fa680bd5815d2dc;hb=c53c53b0280452e1c3a087fbf807b2e508cd66c4;hp=e628908e07f7994a117ff70585fc6c0e54d2377e;hpb=49b8297d25caae7ad4cf1e5208a4a66fdfe071fe;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index e628908..5af8e95 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -58,11 +58,19 @@ AlignCommand::AlignCommand(string option){ //check for required parameters templateFileName = validParameter.validFile(parameters, "template", true); - if (templateFileName == "not found") { cout << "template is a required parameter for the align.seqs command." << endl; abort = true; } + if (templateFileName == "not found") { + mothurOut("template is a required parameter for the align.seqs command."); + mothurOutEndLine(); + abort = true; + } else if (templateFileName == "not open") { abort = true; } candidateFileName = validParameter.validFile(parameters, "candidate", true); - if (candidateFileName == "not found") { cout << "candidate is a required parameter for the align.seqs command." << endl; abort = true; } + if (candidateFileName == "not found") { + mothurOut("candidate is a required parameter for the align.seqs command."); + mothurOutEndLine(); + abort = true; + } else if (candidateFileName == "not open") { abort = true; } //check for optional parameter and set defaults @@ -93,49 +101,45 @@ AlignCommand::AlignCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function AlignCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "AlignCommand", "AlignCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the AlignCommand class function AlignCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** -AlignCommand::~AlignCommand(){ - delete templateDB; - delete alignment; +AlignCommand::~AlignCommand(){ + + if (abort == false) { + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); + delete templateDB; + delete alignment; + } } //********************************************************************************************************************** void AlignCommand::help(){ try { - cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n"; - cout << "The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n"; - cout << "The template and candidate parameters are required." << "\n"; - cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer." << "\n"; - cout << "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"; - cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n"; - cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n"; - cout << "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0." << "\n"; - cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0." << "\n"; - cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0." << "\n"; - cout << "The align.seqs command should be in the following format: " << "\n"; - cout << "align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n"; - cout << "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n"; - cout << "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n"; + mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n"); + mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n"); + mothurOut("The template and candidate parameters are required.\n"); + mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n"); + 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"); + mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7.\n"); + mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"); + mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"); + mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0.\n"); + mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0.\n"); + mothurOut("The align.seqs command should be in the following format: \n"); + mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n"); + mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n"); + mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "AlignCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the AlignCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } @@ -145,14 +149,14 @@ int AlignCommand::execute(){ try { if (abort == true) { return 0; } - srand( (unsigned)time( NULL ) ); //needed to assign names to temporary files - - if(search == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); } else if(search == "suffix") { templateDB = new SuffixDB(templateFileName); } else if(search == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); } else { - cout << search << " is not a valid search option. I will run the command using kmer, ksize=8." << endl; kmerSize = 8; + mothurOut(search + " is not a valid search option. I will run the command using kmer, ksize=8."); + mothurOutEndLine(); + kmerSize = 8; + templateDB = new KmerDB(templateFileName, kmerSize); } @@ -161,7 +165,8 @@ int AlignCommand::execute(){ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); } else if(align == "noalign") { alignment = new NoAlign(); } else { - cout << align << " is not a valid alignment option. I will run the command using needleman." << endl; + mothurOut(align + " is not a valid alignment option. I will run the command using needleman."); + mothurOutEndLine(); alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000); } @@ -181,6 +186,7 @@ int AlignCommand::execute(){ lines.push_back(new linePair(0, numFastaSeqs)); driver(lines[0], alignFileName, reportFileName); + } else{ vector positions; @@ -189,10 +195,12 @@ int AlignCommand::execute(){ ifstream inFASTA; openInputFile(candidateFileName, inFASTA); + string input; while(!inFASTA.eof()){ - char c = inFASTA.get(); - if(c == '>'){ positions.push_back(inFASTA.tellg()); } - while (!inFASTA.eof()) { c = inFASTA.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + getline(inFASTA, input); + if (input.length() != 0) { + if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + } } inFASTA.close(); @@ -219,6 +227,7 @@ int AlignCommand::execute(){ appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName); remove((reportFileName + toString(processIDS[i]) + ".temp").c_str()); } + } #else ifstream inFASTA; @@ -231,21 +240,16 @@ int AlignCommand::execute(){ driver(lines[0], alignFileName, reportFileName); #endif - cout << "It took " << time(NULL) - start << " secs to align " << numFastaSeqs << " sequences" << endl; - cout << endl; - - + mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences."); + mothurOutEndLine(); + mothurOutEndLine(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "AlignCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the AlignCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** @@ -265,7 +269,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){ Sequence* candidateSeq = new Sequence(inFASTA); report.setCandidate(candidateSeq); - Sequence* templateSeq = templateDB->findClosestSequence(candidateSeq); + Sequence temp = templateDB->findClosestSequence(candidateSeq); + Sequence* templateSeq = &temp; + report.setTemplate(templateSeq); report.setSearchParameters(search, templateDB->getSearchScore()); @@ -286,13 +292,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){ return 1; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "AlignCommand", "driver"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the AlignCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /**************************************************************************************************/ @@ -313,7 +315,7 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName) }else if (pid == 0){ driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp"); exit(0); - }else { cout << "unable to spawn the necessary processes." << endl; exit(0); } + }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); } } //force parent to wait until all the processes are done @@ -324,13 +326,9 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName) #endif } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "AlignCommand", "createProcesses"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the AlignCommand class function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /**************************************************************************************************/ @@ -338,34 +336,23 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName) void AlignCommand::appendAlignFiles(string temp, string filename) { try{ - //open output file in append mode ofstream output; - openOutputFileAppend(filename, output); - - //open temp file for reading ifstream input; + openOutputFileAppend(filename, output); openInputFile(temp, input); - string line; - //read input file and write to output file - while(input.eof() != true) { - getline(input, line); //getline removes the newline char - if (line != "") { - output << line << endl; // Appending back newline char - } - } + while(char c = input.get()){ + if(input.eof()) { break; } + else { output << c; } + } input.close(); output.close(); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "AlignCommand", "appendAlignFiles"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the DistanceCommand class function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /**************************************************************************************************/ @@ -373,35 +360,25 @@ void AlignCommand::appendAlignFiles(string temp, string filename) { void AlignCommand::appendReportFiles(string temp, string filename) { try{ - //open output file in append mode ofstream output; - openOutputFileAppend(filename, output); - - //open temp file for reading ifstream input; + openOutputFileAppend(filename, output); openInputFile(temp, input); + while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line - - string line; - //read input file and write to output file - while(input.eof() != true) { - getline(input, line); //getline removes the newline char - if (line != "") { - output << line << endl; // Appending back newline char - } - } + + while(char c = input.get()){ + if(input.eof()) { break; } + else { output << c; } + } input.close(); output.close(); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "AlignCommand", "appendReportFiles"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the DistanceCommand class function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //**********************************************************************************************************************