*/
#include "getsharedotucommand.h"
+#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> GetSharedOTUCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
- CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
- CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(plist);
+ CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter punique("unique", "String", "", "", "", "", "","",false,false,true); parameters.push_back(punique);
+ CommandParameter pshared("shared", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pshared);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
helpString += "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";
helpString += "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";
- helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
- helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+ helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+ helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
}
}
//**********************************************************************************************************************
+string GetSharedOTUCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],[distance],[group],shared.fasta"; }
+ else if (type == "accnos") { pattern = "[filename],[distance],[group],accnos"; }
+ else if (type == "sharedseqs") { pattern = "[filename],[distance],[group],shared.seqs"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(){
try {
abort = true; calledHelp = true;
m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
abort = true;
}
- }else { format = "list"; }
+ }else { format = "list"; m->setListFile(listfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
abort = true;
}
- }
+ }else { m->setGroupFile(groupfile); }
if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
else {
userGroups = "unique." + groups;
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
else {
userGroups = groups;
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
unique = false;
}
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
-
+ else { m->setFastaFile(fastafile); }
}
}
if (m->control_pressed) { delete groupMap; return 0; }
if (Groups.size() == 0) {
- Groups = groupMap->namesOfGroups;
+ Groups = groupMap->getNamesOfGroups();
//make string for outputfile name
userGroups = "unique.";
for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
userGroups = userGroups.substr(0, userGroups.length()-1);
+ }else{
+ //sanity check for group names
+ SharedUtil util;
+ vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, namesOfGroups);
+ groupMap->setNamesOfGroups(namesOfGroups);
}
//put groups in map to find easier
if (m->control_pressed) {
if (lastlist != NULL) { delete lastlist; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete groupMap; return 0;
}
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
if (lastlist != NULL) { delete lastlist; }
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; }
//set fasta file as new current fastafile
string current = "";
string outputFileNames;
if (outputDir == "") { outputDir += m->hasPath(listfile); }
- if (output != "accnos") {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
- }else {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
- }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = shared->getLabel();
+ variables["[group]"] = userGroups;
+ if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
+ else { outputFileNames = getOutputFileName("accnos", variables); }
+
m->openOutputFile(outputFileNames, outNames);
bool wroteSomething = false;
//go through each bin, find out if shared
for (int i = 0; i < shared->getNumBins(); i++) {
- if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
+ if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
bool uniqueOTU = true;
vector<string> namesOfSeqsInThisBin;
- string names = shared->get(i);
- while ((names.find_first_of(',') != -1)) {
- string name = names.substr(0,names.find_first_of(','));
- names = names.substr(names.find_first_of(',')+1, names.length());
+ string names = shared->get(i);
+ vector<string> binNames;
+ m->splitAtComma(names, binNames);
+ for(int j = 0; j < binNames.size(); j++) {
+ string name = binNames[j];
//find group
string seqGroup = groupMap->getGroup(name);
else { atLeastOne[seqGroup]++; }
}
- //get last name
- string seqGroup = groupMap->getGroup(names);
- if (output != "accnos") {
- namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
- }else { namesOfSeqsInThisBin.push_back(names); }
-
- 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);
- if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
- else { atLeastOne[seqGroup]++; }
-
-
//make sure you have at least one seq from each group you want
bool sharedByAll = true;
map<string, int>::iterator it2;
outNames.close();
if (!wroteSomething) {
- remove(outputFileNames.c_str());
+ m->mothurRemove(outputFileNames);
string outputString = "\t" + toString(num) + " - No otus shared by groups";
string groupString = "";
//if fasta file provided output new fasta file
if ((fastafile != "") && wroteSomething) {
if (outputDir == "") { outputDir += m->hasPath(fastafile); }
- string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileFasta = getOutputFileName("fasta", variables);
ofstream outFasta;
m->openOutputFile(outputFileFasta, outFasta);
outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
projects / mothur.git / blobdiff