X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=secondarystructurecommand.cpp;h=dc40611711062150b7046e1be665a34c87d87818;hb=bc4c4d63e983a3e91e74b5038bfec6705e1a3a2e;hp=48ea1549aa78537966745dbe11fbc9d1afbf8f51;hpb=462fca6d24fd15ca035358ff70bcfae52c3281c3;p=mothur.git diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp index 48ea154..dc40611 100644 --- a/secondarystructurecommand.cpp +++ b/secondarystructurecommand.cpp @@ -12,42 +12,72 @@ //********************************************************************************************************************** -AlignCheckCommand::AlignCheckCommand(string option){ +AlignCheckCommand::AlignCheckCommand(string option) { try { abort = false; - + haderror = 0; + //allow user to run help if(option == "help") { help(); abort = true; } else { //valid paramters for this command - string Array[] = {"fasta","map"}; + string Array[] = {"fasta","map", "outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); map parameters = parser.getParameters(); ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("fasta"); + //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["fasta"] = inputDir + it->second; } + } + + it = parameters.find("map"); + //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["map"] = inputDir + it->second; } + } + } + //check for required parameters mapfile = validParameter.validFile(parameters, "map", true); if (mapfile == "not open") { abort = true; } - else if (mapfile == "not found") { mapfile = ""; mothurOut("You must provide an map file."); mothurOutEndLine(); abort = true; } + else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; } fastafile = validParameter.validFile(parameters, "fasta", true); if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true; } + else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true; } + //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 = ""; + outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it + } + } } catch(exception& e) { - errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand"); + m->errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand"); exit(1); } } @@ -55,15 +85,15 @@ AlignCheckCommand::AlignCheckCommand(string option){ void AlignCheckCommand::help(){ try { - //mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group or alignreport file.\n"); - //mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n"); - //mothurOut("The remove.seqs command parameters are accnos, fasta, name, group and alignreport. You must provide accnos and one of the other parameters.\n"); - //mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n"); - //mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n"); - //mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); + m->mothurOut("The align.check command reads a fasta file and map file.\n"); + m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n"); + m->mothurOut("The align.check command parameters are fasta and map, both are required.\n"); + m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n"); + m->mothurOut("Example align.check(map=silva.ss.map, 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) { - errorOut(e, "AlignCheckCommand", "help"); + m->errorOut(e, "AlignCheckCommand", "help"); exit(1); } } @@ -78,13 +108,46 @@ int AlignCheckCommand::execute(){ //get secondary structure info. readMap(); - + ifstream in; + openInputFile(fastafile, in); + + ofstream out; + string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check"; + openOutputFile(outfile, out); + + out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t'; + out << "loop" << '\t' << "tilde" << '\t' << "total" << endl; + + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; } + + Sequence seq(in); gobble(in); + if (seq.getName() != "") { + statData data = getStats(seq.getAligned()); + + if (haderror == 1) { break; } + + out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t'; + out << data.loop << '\t' << data.tilde << '\t' << data.total << endl; + } + } + + in.close(); + out.close(); + + if (m->control_pressed) { remove(outfile.c_str()); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut(outfile); m->mothurOutEndLine(); + m->mothurOutEndLine(); return 0; } catch(exception& e) { - errorOut(e, "AlignCheckCommand", "execute"); + m->errorOut(e, "AlignCheckCommand", "execute"); exit(1); } } @@ -104,7 +167,7 @@ void AlignCheckCommand::readMap(){ gobble(in); } in.close(); - + seqLength = structMap.size(); @@ -112,7 +175,7 @@ void AlignCheckCommand::readMap(){ for(int i=0;imothurOut("Your map file contains an error: line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); m->mothurOutEndLine(); } } } @@ -120,9 +183,77 @@ void AlignCheckCommand::readMap(){ } catch(exception& e) { - errorOut(e, "AlignCheckCommand", "readFasta"); + m->errorOut(e, "AlignCheckCommand", "readMap"); + exit(1); + } +} +/**************************************************************************************************/ + +statData AlignCheckCommand::getStats(string sequence){ + try { + + statData data; + sequence = "*" + sequence; // need to pad the sequence so we can index it by 1 + + int length = sequence.length(); + + if (length != seqLength) { m->mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); m->mothurOutEndLine(); haderror = 1; return data; } + + for(int i=1;ierrorOut(e, "AlignCheckCommand", "getStats"); exit(1); } } + //**********************************************************************************************************************