X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=2e553d96db111a7a0828af855eb7251081014131;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=7af1ac67349843c59a282338387dc127239a1bcb;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp index 7af1ac6..2e553d9 100644 --- a/getsharedotucommand.cpp +++ b/getsharedotucommand.cpp @@ -11,7 +11,7 @@ //********************************************************************************************************************** -GetSharedOTUCommand::GetSharedOTUCommand(string option){ +GetSharedOTUCommand::GetSharedOTUCommand(string option) { try { globaldata = GlobalData::getInstance(); @@ -83,7 +83,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option){ if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } - if ((listfile == "") || (groupfile == "")) { mothurOut("The list and group parameters are required."); mothurOutEndLine(); abort = true; } + if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults // ...at some point should added some additional type checking... @@ -123,7 +123,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option){ } catch(exception& e) { - errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand"); + m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand"); exit(1); } } @@ -131,24 +131,24 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option){ void GetSharedOTUCommand::help(){ try { - mothurOut("The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required.\n"); - mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n"); - mothurOut("The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n"); - mothurOut("If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n"); - mothurOut("If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n"); - mothurOut("If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n"); - mothurOut("The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n"); - mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n"); - mothurOut("With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n"); - mothurOut("The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n"); - mothurOut("The get.sharedseqs command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n"); - mothurOut("Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n"); - mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n"); - mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); + m->mothurOut("The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required.\n"); + m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n"); + m->mothurOut("The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n"); + m->mothurOut("If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n"); + m->mothurOut("If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n"); + m->mothurOut("If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n"); + m->mothurOut("The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n"); + m->mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n"); + m->mothurOut("With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n"); + m->mothurOut("The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n"); + m->mothurOut("The get.sharedseqs command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n"); + m->mothurOut("Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n"); + m->mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n"); + m->mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); } catch(exception& e) { - errorOut(e, "GetSharedOTUCommand", "help"); + m->errorOut(e, "GetSharedOTUCommand", "help"); exit(1); } } @@ -189,7 +189,7 @@ int GetSharedOTUCommand::execute(){ openInputFile(fastafile, inFasta); while(!inFasta.eof()) { - Sequence seq(inFasta); + Sequence seq(inFasta); gobble(inFasta); if (seq.getName() != "") { seqs.push_back(seq); } } inFasta.close(); @@ -211,7 +211,7 @@ int GetSharedOTUCommand::execute(){ list = new ListVector(in); if(allLines == 1 || labels.count(list->getLabel()) == 1){ - mothurOut(list->getLabel()); + m->mothurOut(list->getLabel()); process(list); processedLabels.insert(list->getLabel()); @@ -221,7 +221,7 @@ int GetSharedOTUCommand::execute(){ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); - mothurOut(lastlist->getLabel()); + m->mothurOut(lastlist->getLabel()); process(lastlist); processedLabels.insert(lastlist->getLabel()); @@ -243,18 +243,18 @@ int GetSharedOTUCommand::execute(){ set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } //run last label if you need to if (needToRun == true) { - mothurOut(lastlist->getLabel()); + m->mothurOut(lastlist->getLabel()); process(lastlist); processedLabels.insert(lastlist->getLabel()); @@ -266,11 +266,19 @@ int GetSharedOTUCommand::execute(){ globaldata->Groups.clear(); if (lastlist != NULL) { delete lastlist; } + + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + + return 0; } catch(exception& e) { - errorOut(e, "GetSharedOTUCommand", "execute"); + m->errorOut(e, "GetSharedOTUCommand", "execute"); exit(1); } } @@ -300,8 +308,8 @@ void GetSharedOTUCommand::process(ListVector* shared) { bool uniqueOTU = true; map atLeastOne; - for (int m = 0; m < Groups.size(); m++) { - atLeastOne[Groups[m]] = 0; + for (int f = 0; f < Groups.size(); f++) { + atLeastOne[Groups[f]] = 0; } vector namesOfSeqsInThisBin; @@ -317,7 +325,7 @@ void GetSharedOTUCommand::process(ListVector* shared) { namesOfSeqsInThisBin.push_back((name + "\t" + seqGroup + "\t" + toString(i+1))); }else { namesOfSeqsInThisBin.push_back(name); } - if (seqGroup == "not found") { mothurOut(name + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1); } + if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); } //is this seq in one of hte groups we care about it = groupFinder.find(seqGroup); @@ -331,7 +339,7 @@ void GetSharedOTUCommand::process(ListVector* shared) { namesOfSeqsInThisBin.push_back((names + "\t" + seqGroup + "\t" + toString(i+1))); }else { namesOfSeqsInThisBin.push_back(names); } - if (seqGroup == "not found") { mothurOut(names + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1); } + if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); } //is this seq in one of hte groups we care about it = groupFinder.find(seqGroup); @@ -382,8 +390,11 @@ void GetSharedOTUCommand::process(ListVector* shared) { } outputString += groupString + "."; - mothurOut(outputString); mothurOutEndLine(); - }else { mothurOut("\t" + toString(num)); mothurOutEndLine(); } + m->mothurOut(outputString); m->mothurOutEndLine(); + }else { + m->mothurOut("\t" + toString(num)); m->mothurOutEndLine(); + outputNames.push_back(outputFileNames); + } //if fasta file provided output new fasta file if ((fastafile != "") && wroteSomething) { @@ -391,6 +402,7 @@ void GetSharedOTUCommand::process(ListVector* shared) { string outputFileFasta = outputDir + getRootName(getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta"; ofstream outFasta; openOutputFile(outputFileFasta, outFasta); + outputNames.push_back(outputFileFasta); for (int k = 0; k < seqs.size(); k++) { //if this is a sequence we want, output it @@ -404,7 +416,7 @@ void GetSharedOTUCommand::process(ListVector* shared) { } outFasta << seqs[k].getAligned() << endl; - }else { mothurOut(seqs[k].getName() + " is not in your fasta file. Please correct."); mothurOutEndLine(); } + } } outFasta.close(); @@ -413,7 +425,7 @@ void GetSharedOTUCommand::process(ListVector* shared) { } catch(exception& e) { - errorOut(e, "GetSharedOTUCommand", "process"); + m->errorOut(e, "GetSharedOTUCommand", "process"); exit(1); } }