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|
//
// makebiomcommand.cpp
// Mothur
//
// Created by Sarah Westcott on 4/16/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "makebiomcommand.h"
#include "inputdata.h"
#include "phylotree.h"
//taken from http://biom-format.org/documentation/biom_format.html
/* Minimal Sparse
{
"id":null,
"format": "Biological Observation Matrix 0.9.1",
"format_url": "http://biom-format.org",
"type": "OTU table",
"generated_by": "QIIME revision 1.4.0-dev",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":null},
{"id":"GG_OTU_2", "metadata":null},
{"id":"GG_OTU_3", "metadata":null},
{"id":"GG_OTU_4", "metadata":null},
{"id":"GG_OTU_5", "metadata":null}
],
"columns": [
{"id":"Sample1", "metadata":null},
{"id":"Sample2", "metadata":null},
{"id":"Sample3", "metadata":null},
{"id":"Sample4", "metadata":null},
{"id":"Sample5", "metadata":null},
{"id":"Sample6", "metadata":null}
],
"matrix_type": "sparse",
"matrix_element_type": "int",
"shape": [5, 6],
"data":[[0,2,1],
[1,0,5],
[1,1,1],
[1,3,2],
[1,4,3],
[1,5,1],
[2,2,1],
[2,3,4],
[2,4,2],
[3,0,2],
[3,1,1],
[3,2,1],
[3,5,1],
[4,1,1],
[4,2,1]
]
}
*/
/* Minimal dense
{
"id":null,
"format": "Biological Observation Matrix 0.9.1",
"format_url": "http://biom-format.org",
"type": "OTU table",
"generated_by": "QIIME revision 1.4.0-dev",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":null},
{"id":"GG_OTU_2", "metadata":null},
{"id":"GG_OTU_3", "metadata":null},
{"id":"GG_OTU_4", "metadata":null},
{"id":"GG_OTU_5", "metadata":null}
],
"columns": [
{"id":"Sample1", "metadata":null},
{"id":"Sample2", "metadata":null},
{"id":"Sample3", "metadata":null},
{"id":"Sample4", "metadata":null},
{"id":"Sample5", "metadata":null},
{"id":"Sample6", "metadata":null}
],
"matrix_type": "dense",
"matrix_element_type": "int",
"shape": [5,6],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
}
*/
//**********************************************************************************************************************
vector<string> MakeBiomCommand::setParameters(){
try {
CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","biom",false,false,true); parameters.push_back(pshared);
CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","biom",false,false,true); parameters.push_back(prelabund);
CommandParameter pcontaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcontaxonomy);
CommandParameter preference("reftaxonomy", "InputTypes", "", "", "none", "none", "refPi","",false,false); parameters.push_back(preference);
CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter ppicrust("picrust", "InputTypes", "", "", "none", "none", "refPi","shared",false,false); parameters.push_back(ppicrust);
CommandParameter poutput("output", "Multiple", "simple-hdf5", "hdf5", "", "", "","",false,false, true); parameters.push_back(poutput);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
CommandParameter pmatrixtype("matrixtype", "Multiple", "sparse-dense", "sparse", "", "", "","",false,false); parameters.push_back(pmatrixtype);
abort = false; calledHelp = false; allLines = true;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["biom"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
outputTypes["relabund"] = tempOutNames;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string MakeBiomCommand::getHelpString(){
try {
string helpString = "";
helpString += "The make.biom command parameters are shared, relabund, contaxonomy, metadata, groups, matrixtype, picrust, reftaxonomy and label. shared or relabund are required, unless you have a valid current file.\n"; //
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
helpString += "The matrixtype parameter allows you to select what type you would like to make. Choices are sparse and dense, default is sparse.\n";
helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance. ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled. It is used to assign taxonomy information to the metadata of rows.\n";
helpString += "The metadata parameter is used to provide experimental parameters to the columns. Things like 'sample1 gut human_gut'. \n";
helpString += "The picrust parameter is used to provide the greengenes OTU IDs map table. NOTE: Picrust requires a greengenes taxonomy. \n";
helpString += "The referencetax parameter is used with the picrust parameter. Picrust requires the greengenes OTU IDs to be in the biom file. \n";
helpString += "The output parameter allows you to specify format of your biom file. Options hdf5 or simple. Default is hdf5, unless you are running a version without HDF5 libraries.\n";
helpString += "The make.biom command should be in the following format: make.biom(shared=yourShared, groups=yourGroups, label=yourLabels).\n";
helpString += "Example make.biom(shared=abrecovery.an.shared, groups=A-B-C).\n";
helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
helpString += "The make.biom command outputs a .biom file.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string MakeBiomCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "biom") { pattern = "[filename],[distance],biom"; }
else if (type == "shared") { pattern = "[filename],[distance],biom_shared"; }
else if (type == "relabund") { pattern = "[filename],[distance],biom_relabund"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
MakeBiomCommand::MakeBiomCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
relabundfile = validParameter.validFile(parameters, "relabund");
if (relabundfile == "not open") { abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
else { inputFileName = relabundfile; fileFormat = "relabund"; current->setRelAbundFile(relabundfile); }
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { inputFileName = sharedfile; fileFormat = "sharedfile"; current->setSharedFile(sharedfile); }
if ((relabundfile == "") && (sharedfile == "")) {
//is there are current file available for either of these?
//give priority to shared, then relabund
sharedfile = current->getSharedFile();
if (sharedfile != "") { inputFileName = sharedfile; fileFormat="sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else {
relabundfile = current->getRelAbundFile();
if (relabundfile != "") { inputFileName = relabundfile; fileFormat="relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter.\n"); }
else {
m->mothurOut("No valid current files. You must provide a shared or relabund.\n"); abort = true;
}
}
}
if (outputdir == ""){ outputdir = util.hasPath(inputFileName); }
contaxonomyfile = validParameter.validFile(parameters, "constaxonomy");
if (contaxonomyfile == "not found") { contaxonomyfile = ""; }
else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
referenceTax = validParameter.validFile(parameters, "reftaxonomy");
if (referenceTax == "not found") { referenceTax = ""; }
else if (referenceTax == "not open") { referenceTax = ""; abort = true; }
picrustOtuFile = validParameter.validFile(parameters, "picrust");
if (picrustOtuFile == "not found") { picrustOtuFile = ""; }
else if (picrustOtuFile == "not open") { picrustOtuFile = ""; abort = true; }
metadatafile = validParameter.validFile(parameters, "metadata");
if (metadatafile == "not found") { metadatafile = ""; }
else if (metadatafile == "not open") { metadatafile = ""; abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
groups = validParameter.valid(parameters, "groups");
if (groups == "not found") { groups = ""; }
else {
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
if (picrustOtuFile != "") {
picrust=true;
if (contaxonomyfile == "") { m->mothurOut("[ERROR]: the constaxonomy parameter is required with the picrust parameter, aborting.\n"); abort = true; }
if (referenceTax == "") { m->mothurOut("[ERROR]: the reftaxonomy parameter is required with the picrust parameter, aborting.\n"); abort = true; }
}else { picrust=false; }
if ((contaxonomyfile != "") && (labels.size() > 1)) { m->mothurOut("[ERROR]: the contaxonomy parameter cannot be used with multiple labels.\n"); abort = true; }
format = validParameter.valid(parameters, "matrixtype"); if (format == "not found") { format = "sparse"; }
if ((format != "sparse") && (format != "dense")) {
m->mothurOut(format + " is not a valid option for the matrixtype parameter. Options are sparse and dense.\n"); abort = true;
}
output = validParameter.valid(parameters, "output");
if (output == "not found") {
#ifdef USE_HDF5
output = "hdf5";
#else
output = "simple";
#endif
}
if ((output != "hdf5") && (output != "simple")) {
m->mothurOut("Invalid option for output. output options are hdf5 and simple, quitting.\n"); abort = true;
}
if (output == "hdf5") {
#ifdef USE_HDF5
//do nothing we have the api
#else
m->mothurOut("[ERROR]: To write HDF5 biom files, you must have the API installed, quitting.\n"); abort=true;
#endif
}
}
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "MakeBiomCommand");
exit(1);
}
}
//**********************************************************************************************************************
int MakeBiomCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
SharedRAbundVectors* lookup = nullptr; SharedRAbundFloatVectors* lookupRel = nullptr;
InputData input(inputFileName, fileFormat, Groups);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
vector<string> sampleMetadata;
if (fileFormat == "sharedfile") {
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
sampleMetadata = getSampleMetaData(lookup);
}else {
lookupRel = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookupRel->getNamesGroups();
sampleMetadata = getSampleMetaData(lookupRel);
}
//if user did not specify a label, then use first one
if ((contaxonomyfile != "") && (labels.size() == 0)) { allLines = false; labels.insert(lastLabel); }
Picrust* piCrust = nullptr;
if (picrust) { piCrust = new Picrust(referenceTax, picrustOtuFile); }
vector<Taxonomy> consTax;
if (contaxonomyfile != "") { util.readConsTax(contaxonomyfile, consTax); }
if (fileFormat == "sharedfile") {
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
getBiom(lookup, piCrust, consTax, sampleMetadata); delete lookup;
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
}
}else {
while (lookupRel != nullptr) {
if (m->getControl_pressed()) { delete lookupRel; break; }
getBiom(lookupRel, piCrust, consTax, sampleMetadata); delete lookupRel;
lookupRel = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
}
}
if (picrust) { delete piCrust; }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
//set sabund file as new current sabundfile
string currentName = "";
itTypes = outputTypes.find("biom");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setBiomFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
void MakeBiomCommand::getBiom(SharedRAbundVectors*& lookup, Picrust* picrust, vector<Taxonomy> consTax, vector<string> sampleMetadata){
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(sharedfile));
variables["[distance]"] = lookup->getLabel();
string outputFileName = getOutputFileName("biom",variables);
outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
string mothurString = "mothur_" + toString(current->getVersion());
Biom* biom;
if (output == "hdf5") { biom = new BiomHDF5(); }
else { biom = new BiomSimple(); }
biom->load(lookup, consTax);
biom->fillHeading(mothurString, sharedfile);
biom->print(outputFileName, sampleMetadata, picrust);
if (picrust) {
string outputFileName2 = getOutputFileName("shared",variables);
outputNames.push_back(outputFileName2); outputTypes["shared"].push_back(outputFileName2);
ofstream out2; util.openOutputFile(outputFileName2, out2); bool printHeaders = true;
biom->getSharedRAbundVectors()->print(out2, printHeaders);
out2.close();
}
delete biom;
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "getBiom");
exit(1);
}
}
//**********************************************************************************************************************
void MakeBiomCommand::getBiom(SharedRAbundFloatVectors*& lookup, Picrust* picrust, vector<Taxonomy> consTax, vector<string> sampleMetadata){
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputFileName));
variables["[distance]"] = lookup->getLabel();
string outputFileName = getOutputFileName("biom",variables);
outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
string mothurString = "mothur_" + toString(current->getVersion());
BiomSimple biom; biom.load(lookup, consTax);
biom.fillHeading(mothurString, sharedfile);
biom.print(outputFileName, sampleMetadata, picrust);
if (picrust) {
string outputFileName2 = getOutputFileName("relabund",variables);
outputNames.push_back(outputFileName2); outputTypes["relabund"].push_back(outputFileName2);
ofstream out2; util.openOutputFile(outputFileName2, out2); bool printHeaders = true;
biom.getSharedRAbundFloatVectors()->print(out2, printHeaders);
out2.close();
}
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "getBiom");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> MakeBiomCommand::getSampleMetaData(SharedRAbundVectors*& lookup){
try {
vector<string> sampleMetadata;
if (metadatafile == "") { for (int i = 0; i < lookup->size(); i++) { sampleMetadata.push_back("null"); } }
else {
ifstream in; util.openInputFile(metadatafile, in);
vector<string> groupNames, metadataLabels;
map<string, vector<string> > lines;
string headerLine = util.getline(in); gobble(in);
vector<string> pieces = util.splitWhiteSpace(headerLine);
//save names of columns you are reading
for (int i = 1; i < pieces.size(); i++) {
metadataLabels.push_back(pieces[i]);
}
int count = metadataLabels.size();
//read rest of file
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
string group = "";
in >> group; gobble(in);
groupNames.push_back(group);
string line = util.getline(in); gobble(in);
vector<string> thisPieces = util.splitWhiteSpaceWithQuotes(line);
if (m->getDebug()) { m->mothurOut("[DEBUG]: " + group + " " + util.getStringFromVector(thisPieces, ", ") + "\n"); }
if (thisPieces.size() != count) { m->mothurOut("[ERROR]: expected " + toString(count) + " items of data for sample " + group + " read " + toString(thisPieces.size()) + ", quitting.\n"); }
else { if (util.inUsersGroups(group, Groups)) { lines[group] = thisPieces; } }
gobble(in);
}
in.close();
map<string, vector<string> >::iterator it;
vector<string> namesOfGroups = lookup->getNamesGroups();
for (int i = 0; i < namesOfGroups.size(); i++) {
if (m->getControl_pressed()) { break; }
it = lines.find(namesOfGroups[i]);
if (it == lines.end()) { m->mothurOut("[ERROR]: can't find metadata information for " + namesOfGroups[i] + ", quitting.\n"); m->setControl_pressed(true); }
else {
vector<string> values = it->second;
string data = "{";
for (int j = 0; j < metadataLabels.size()-1; j++) {
values[j] = util.removeQuotes(values[j]);
data += "\"" + metadataLabels[j] + "\":\"" + values[j] + "\", ";
}
values[metadataLabels.size()-1] = util.removeQuotes(values[metadataLabels.size()-1]);
data += "\"" + metadataLabels[metadataLabels.size()-1] + "\":\"" + values[metadataLabels.size()-1] + "\"}";
sampleMetadata.push_back(data);
}
}
}
return sampleMetadata;
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "getSampleMetaData");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> MakeBiomCommand::getSampleMetaData(SharedRAbundFloatVectors*& lookup){
try {
vector<string> sampleMetadata;
if (metadatafile == "") { for (int i = 0; i < lookup->size(); i++) { sampleMetadata.push_back("null"); } }
else {
ifstream in; util.openInputFile(metadatafile, in);
vector<string> groupNames, metadataLabels;
map<string, vector<string> > lines;
string headerLine = util.getline(in); gobble(in);
vector<string> pieces = util.splitWhiteSpace(headerLine);
//save names of columns you are reading
for (int i = 1; i < pieces.size(); i++) {
metadataLabels.push_back(pieces[i]);
}
int count = metadataLabels.size();
//read rest of file
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
string group = "";
in >> group; gobble(in);
groupNames.push_back(group);
string line = util.getline(in); gobble(in);
vector<string> thisPieces = util.splitWhiteSpaceWithQuotes(line);
if (thisPieces.size() != count) { m->mothurOut("[ERROR]: expected " + toString(count) + " items of data for sample " + group + " read " + toString(thisPieces.size()) + ", quitting.\n"); }
else { if (util.inUsersGroups(group, Groups)) { lines[group] = thisPieces; } }
gobble(in);
}
in.close();
map<string, vector<string> >::iterator it;
vector<string> namesOfGroups = lookup->getNamesGroups();
for (int i = 0; i < namesOfGroups.size(); i++) {
if (m->getControl_pressed()) { break; }
it = lines.find(namesOfGroups[i]);
if (it == lines.end()) { m->mothurOut("[ERROR]: can't find metadata information for " + namesOfGroups[i] + ", quitting.\n"); m->setControl_pressed(true); }
else {
vector<string> values = it->second;
string data = "{";
for (int j = 0; j < metadataLabels.size()-1; j++) {
values[j] = util.removeQuotes(values[j]);
data += "\"" + metadataLabels[j] + "\":\"" + values[j] + "\", ";
}
values[metadataLabels.size()-1] = util.removeQuotes(values[metadataLabels.size()-1]);
data += "\"" + metadataLabels[metadataLabels.size()-1] + "\":\"" + values[metadataLabels.size()-1] + "\"}";
sampleMetadata.push_back(data);
}
}
}
return sampleMetadata;
}
catch(exception& e) {
m->errorOut(e, "MakeBiomCommand", "getSampleMetaData");
exit(1);
}
}
/**************************************************************************************************/
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