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325 lines (257 loc) · 14.7 KB
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/*****************************************************************************
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 INRIA
* Authors: R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/********************************************************************************/
// We include required definitions
/********************************************************************************/
#include <Minia.hpp>
#include <gatb/debruijn/impl/Simplifications.hpp>
#include <gatb/debruijn/impl/GraphUnitigs.hpp>
#include <fstream>
#include <iomanip> // for setprecision
using namespace std;
/********************************************************************************/
#define DEBUG(a) //a
/********************************************************************************/
static const char* STR_TRAVERSAL_KIND = "-traversal";
static const char* STR_FASTA_LINE_SIZE = "-fasta-line";
static const char* STR_KEEP_ISOLATED = "-keep-isolated";
static const char* progressFormat0 = "Minia : assembly";
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
Minia::Minia () : Tool ("minia")
{
#ifdef GIT_SHA1
std::cout << "Minia 3, git commit " << GIT_SHA1 << std::endl;
#endif
// reinit the parser to get rid of options added by the Tool class, as we'll add them again in the Graph parser
setParser (new OptionsParser ("minia"));
/** We add options specific to Minia (most important at the end). */
OptionsParser* assemblyParser = new OptionsParser ("assembly");
assemblyParser->push_front (new OptionOneParam (STR_FASTA_LINE_SIZE, "number of nucleotides per line in fasta output (0 means one line)", false, "0"));
assemblyParser->push_front (new OptionOneParam (STR_TRAVERSAL_KIND, "traversal type ('contig', 'unitig')", false, "contig" ));
assemblyParser->push_front (new OptionNoParam (STR_KEEP_ISOLATED, "keep short (<= max(2k, 150 bp)) isolated output sequences", false));
assemblyParser->push_front (new OptionOneParam (STR_URI_INPUT, "input reads (fasta/fastq/compressed) or hdf5 file", false));
getParser()->push_back (assemblyParser);
OptionsParser* simplificationsParser = new OptionsParser ("graph simplifications");
// this requires that Minia is compiled to support kmer values of 32 at least.
Simplifications<GraphUnitigsTemplate<32>,NodeGU,EdgeGU> graphSimplifications(nullptr, 1, false); // get a graph simplifications object just to get default parameters
simplificationsParser->push_back (new OptionNoParam ("-no-bulge-removal", "ask to not perform bulge removal", false));
simplificationsParser->push_back (new OptionNoParam ("-no-tip-removal", "ask to not perform tip removal", false));
simplificationsParser->push_back (new OptionNoParam ("-no-ec-removal", "ask to not perform erroneous connection removal", false));
simplificationsParser->push_back (new OptionOneParam ("-tip-len-topo-kmult", "remove all tips of length <= k * X bp", false, to_string(graphSimplifications._tipLen_Topo_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-tip-len-rctc-kmult", "remove tips that pass coverage criteria, of length <= k * X bp", false, to_string(graphSimplifications._tipLen_RCTC_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-tip-rctc-cutoff", "tip relative coverage coefficient: mean coverage of neighbors > X * tip coverage", false, to_string(graphSimplifications._tipRCTCcutoff)));
simplificationsParser->push_back (new OptionOneParam ("-bulge-len-kmult", "bulges shorter than k*X bp are candidate to be removed", false, to_string(graphSimplifications._bulgeLen_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-bulge-len-kadd", "bulges shorter than k+X bp are candidate to be removed", false, to_string(graphSimplifications._bulgeLen_kAdd)));
simplificationsParser->push_back (new OptionOneParam ("-bulge-altpath-kadd", "explore up to k+X nodes to find alternative path", false, to_string(graphSimplifications._bulgeAltPath_kAdd))); // TODO k should not appear in that equation
simplificationsParser->push_back (new OptionOneParam ("-bulge-altpath-covmult", "bulges of coverage <= X*cov_altpath will be removed", false, to_string(graphSimplifications._bulgeAltPath_covMult)));
simplificationsParser->push_back (new OptionOneParam ("-ec-len-kmult", "EC shorter than k*X bp are candidates to be removed", false, to_string(graphSimplifications._ecLen_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-ec-rctc-cutoff", "EC relative coverage coefficient (similar in spirit as tip)", false, to_string(graphSimplifications._ecRCTCcutoff)));
getParser()->push_back (simplificationsParser);
// when we input reads, dbgh5 is executed, so its options are needed here
IOptionsParser* graphParser = Graph::getOptionsParser(false);
// we hide the STR_URI_INPUT option, otherwise we would have it twice
if (IOptionsParser* p = graphParser->getParser(STR_URI_INPUT)) { p->setVisible(false); }
// we set the default value for the abundance min (2)
if (Option* p = dynamic_cast<Option*> (graphParser->getParser(STR_KMER_ABUNDANCE_MIN))) { p->setDefaultValue ("2"); }
// through an undocumented environment variable, we can set the temporary path (useful to not have to specify -out-tmp every time)
char *hidden_env_variable_out_tmp = std::getenv("MINIA_OUT_TMP");
if (hidden_env_variable_out_tmp)
{
if (Option* p = dynamic_cast<Option*> (graphParser->getParser(STR_URI_OUTPUT_TMP))) { p->setDefaultValue ((string)hidden_env_variable_out_tmp); }
}
getParser()->push_back(graphParser, 1);
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
struct Parameter
{
Parameter (Minia& minia) : minia(minia){}
Minia& minia;
};
template<size_t span>
struct MiniaFunctor { void operator () (Parameter parameter)
{
Minia& minia = parameter.minia;
// selection of type of graph is done HERE
//typedef GraphTemplate<NodeFast<span>,EdgeFast<span>,GraphDataVariantFast<span>> GraphType;
typedef GraphUnitigsTemplate<span> GraphType;
GraphType graph;
{
TIME_INFO (minia.getTimeInfo(), "graph construction");
if (minia.getInput()->get(STR_URI_INPUT) != 0)
{
graph = GraphType::create (minia.getInput());
}
else
{
throw OptionFailure (minia.getParser(), "Specifiy -in");
}
}
/** We build the contigs. */
string output = minia.assemble<GraphType, NodeGU, EdgeGU, span>(graph);
// link contigs
uint nb_threads = 1; // doesn't matter because for now link_tigs is single-threaded
bool verbose = true;
link_tigs<span>(output, minia.k, nb_threads, minia.nbContigs, verbose, false);
/** We gather some statistics. */
minia.getInfo()->add (1, minia.getTimeInfo().getProperties("time"));
}
};
void Minia::execute ()
{
/** we get the kmer size chosen by the end user. */
k = getInput()->getInt (STR_KMER_SIZE);
/** We launch Minia with the correct Integer implementation according to the choosen kmer size. */
Integer::apply<MiniaFunctor,Parameter> (k, Parameter (*this));
}
template <typename Graph_type, typename Node, typename Edge, size_t span>
void Minia::assembleFrom(Node startingNode, Graph_type& graph, IBank *outputBank)
{
unsigned int isolatedCutoff = std::max(2*(unsigned int)graph.getKmerSize(), (unsigned int)150);
bool isolatedLeft, isolatedRight;
float coverage = 0;
string sequence = graph.simplePathBothDirections(startingNode, isolatedLeft, isolatedRight, true, coverage);
Sequence seq (Data::ASCII);
seq.getData().setRef ((char*)sequence.c_str(), sequence.size());
/** We set the sequence comment. */
stringstream ss1;
// spades-like header (compatible with bandage)
//ss1 << "NODE_"<< nbContigs + 1 << "_length_" << sequence.size() << "_cov_" << fixed << std::setprecision(3) << coverage << "_ID_" << nbContigs;
// bcalm-like header (that can be converted to GFA)
ss1 << nbContigs << " LN:i:" << sequence.size() << " KC:i:" << (unsigned int)(coverage*(sequence.size()-k+1)) << " km:f:" << fixed << std::setprecision(3) << coverage ;
seq._comment = ss1.str();
unsigned int lenTotal = sequence.size();
if (lenTotal > isolatedCutoff || (lenTotal <= isolatedCutoff && (!(isolatedLeft && isolatedRight))) || keepIsolatedTigs)
{
outputBank->insert (seq);
nbContigs += 1;
totalNt += lenTotal;
if (lenTotal > maxContigLen) { maxContigLen = lenTotal; }
}
else
nbSmallContigs++;
return;
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
template <typename Graph_type, typename Node, typename Edge, size_t span>
string Minia::assemble (/*const, removed because Simplifications isn't const anymore*/ Graph_type& graph)
{
TIME_INFO (getTimeInfo(), "assembly");
string output = (getInput()->get(STR_URI_OUTPUT) ?
getInput()->getStr(STR_URI_OUTPUT) :
System::file().getBaseName (getInput()->getStr(STR_URI_INPUT))
)+ ".contigs.fa";
/** We create the output bank. Note that we could make this a little bit prettier
* => possibility to save the contigs in specific output format (other than fasta). */
IBank* outputBank = new BankFasta (output);
LOCAL (outputBank);
/** We set the fasta line size. */
BankFasta::setDataLineSize (getInput()->getInt (STR_FASTA_LINE_SIZE));
bool simplifyGraph = false;
string traversalKind = "unitig"; // we output unitigs of the simplified graph or the original graph
simplifyGraph = getInput()->getStr(STR_TRAVERSAL_KIND).compare("contig") == 0;
nbContigs = 0;
nbSmallContigs = 0;
totalNt = 0;
maxContigLen = 0;
keepIsolatedTigs = getParser()->saw(STR_KEEP_ISOLATED);
string str_tipRemoval = "", str_bubbleRemoval = "", str_ECRemoval = "";
/** We get an iterator over all nodes . */
ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> itNode (graph.Graph_type::iterator(), progressFormat0);
// if we want unitigs, then don't simplify the graph; else do it
if (simplifyGraph)
{
int nbCores = getInput()->getInt(STR_NB_CORES);
bool verbose=true;
Simplifications<Graph_type,Node,Edge> graphSimplifications(&graph, nbCores, verbose);
if (getParser()->saw("-no-tip-removal"))
graphSimplifications._doTipRemoval = false;
if (getParser()->saw("-no-bulge-removal"))
graphSimplifications._doBulgeRemoval = false;
if (getParser()->saw("-no-ec-removal"))
graphSimplifications._doECRemoval = false;
if (getParser()->saw("-tip-len-topo-kmult"))
graphSimplifications._tipLen_Topo_kMult = getInput()->getDouble("-tip-len-topo-kmult");
if (getParser()->saw("-tip-len-rctc-kmult"))
graphSimplifications._tipLen_RCTC_kMult = getInput()->getDouble("-tip-len-rctc-kmult");
if (getParser()->saw("-tip-rctc-cutoff"))
graphSimplifications._tipRCTCcutoff = getInput()->getDouble("-tip-rctc-cutoff");
if (getParser()->saw("-bulge-len-kmult"))
graphSimplifications._bulgeLen_kMult = getInput()->getDouble("-bulge-len-kmult");
if (getParser()->saw("-bulge-len-kadd"))
graphSimplifications._bulgeLen_kAdd = getInput()->getDouble("-bulge-len-kadd");
if (getParser()->saw("-bulge-altpath-kadd"))
graphSimplifications._bulgeAltPath_kAdd = getInput()->getDouble("-bulge-altpath-kadd");
if (getParser()->saw("-bulge-altpath-covmult"))
graphSimplifications._bulgeAltPath_covMult = getInput()->getDouble("-bulge-altpath-covmult");
if (getParser()->saw("-ec-len-kmult"))
graphSimplifications._ecLen_kMult = getInput()->getDouble("-ec-len-kmult");
if (getParser()->saw("-ec-rctc-cutoff"))
graphSimplifications._ecRCTCcutoff = getInput()->getDouble("-ec-rctc-cutoff");
graphSimplifications.simplify();
str_tipRemoval = graphSimplifications.tipRemoval;
str_bubbleRemoval = graphSimplifications.bubbleRemoval;
str_ECRemoval = graphSimplifications.ECRemoval;
}
//graph.debugPrintAllUnitigs(); // debugging
/** We loop over all nodes. */
for (itNode.first(); !itNode.isDone(); itNode.next())
{
Node node = itNode.item();
if (graph.unitigIsMarked(node)) { continue; }
if (graph.isNodeDeleted(node)) { continue; }
DEBUG ((cout << endl << "-------------------------- " << graph.toString (node) << " -------------------------" << endl));
assembleFrom<Graph_type, Node, Edge, span>(node, graph, outputBank);
}
/** We add the input parameters to the global properties. */
getInfo()->add (1, getInput());
/** We gather some statistics. */
getInfo()->add (1, "stats");
getInfo()->add (2, "traversal", "%s", getInput()->getStr(STR_TRAVERSAL_KIND).c_str());
getInfo()->add (2, "nb_contigs", "%d", nbContigs);
getInfo()->add (2, "nb_small_contigs_discarded","%d", nbSmallContigs);
getInfo()->add (2, "nt_assembled", "%ld", totalNt);
getInfo()->add (2, "max_length", "%d", maxContigLen);
getInfo()->add (2, "graph simpification stats");
getInfo()->add (3, "tips removed", "%s", str_tipRemoval.c_str());
getInfo()->add (3, "bulges removed", "%s", str_bubbleRemoval.c_str());
getInfo()->add (3, "EC removed", "%s", str_ECRemoval.c_str());
getInfo()->add (2, "assembly traversal stats");
return output;
}