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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 <NodeSelector.hpp>
#include <fstream>
using namespace std;
/********************************************************************************/
#define DEBUG(a) //a
/********************************************************************************/
static const char* STR_TRAVERSAL_KIND = "-traversal";
static const char* STR_STARTER_KIND = "-starter";
static const char* STR_CONTIG_MAX_LEN = "-contig-max-len";
static const char* STR_BFS_MAX_DEPTH = "-bfs-max-depth";
static const char* STR_BFS_MAX_BREADTH = "-bfs-max-breadth";
static const char* STR_NO_LENGTH_CUTOFF = "-no-length-cutoff";
static const char* STR_FASTA_LINE_SIZE = "-fasta-line";
static const char* progressFormat0 = "Assembly ";
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
Minia::Minia () : Tool ("minia")
{
// 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_BFS_MAX_BREADTH, "maximum breadth for BFS", false, "0" ));
assemblyParser->push_front (new OptionOneParam (STR_BFS_MAX_DEPTH, "maximum depth for BFS", false, "0" ));
assemblyParser->push_front (new OptionOneParam (STR_CONTIG_MAX_LEN, "maximum length for contigs", false, "0" ));
assemblyParser->push_front (new OptionOneParam (STR_STARTER_KIND, "starting node ('best', 'simple')", false, "best" ));
assemblyParser->push_front (new OptionOneParam (STR_TRAVERSAL_KIND, "traversal type ('contig', 'unitig')", false, "contig" ));
assemblyParser->push_front (new OptionNoParam (STR_NO_LENGTH_CUTOFF, "turn off length cutoff of 2*k in output sequences", false));
assemblyParser->push_front (new OptionOneParam (STR_URI_INPUT, "input reads (fasta/fastq/compressed)", false));
assemblyParser->push_front (new OptionOneParam (STR_URI_GRAPH, "input graph file (hdf5)", false));
getParser()->push_back (assemblyParser);
// when we input reads, dbgh5 is executed, so its options are needed here
IOptionsParser* graphParser = Graph::getOptionsParser(false, true);
// we hide the STR_URI_INPUT option, otherwise we would have it twice
if (IOptionsParser* p = graphParser->getParser(STR_URI_INPUT)) { p->setVisible(false); }
getParser()->push_back(graphParser, 1);
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
void Minia::execute ()
{
Graph graph;
if (getInput()->get(STR_URI_GRAPH) != 0)
{
graph = Graph::load (getInput()->getStr(STR_URI_GRAPH));
}
else if (getInput()->get(STR_URI_INPUT) != 0)
{
graph = Graph::create (getInput());
}
else
{
throw OptionFailure (getParser(), "Specifiy -graph or -in");
}
/** We build the contigs. */
assemble (graph);
/** We gather some statistics. */
getInfo()->add (1, getTimeInfo().getProperties("time"));
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
void Minia::assemble (const Graph& graph)
{
TIME_INFO (getTimeInfo(), "assembly");
string output = (getInput()->get(STR_URI_OUTPUT) ?
getInput()->getStr(STR_URI_OUTPUT) :
System::file().getBaseName (
(getInput()->get(STR_URI_INPUT) ? getInput()->getStr(STR_URI_INPUT) :
getInput()->getStr(STR_URI_GRAPH))
)
)+ ".contigs.fa";
/** We setup default values if needed. */
if (getInput()->getInt (STR_CONTIG_MAX_LEN) == 0) { getInput()->setInt (STR_CONTIG_MAX_LEN, Traversal::defaultMaxLen); }
if (getInput()->getInt (STR_BFS_MAX_DEPTH) == 0) { getInput()->setInt (STR_BFS_MAX_DEPTH, Traversal::defaultMaxDepth); }
if (getInput()->getInt (STR_BFS_MAX_BREADTH) == 0) { getInput()->setInt (STR_BFS_MAX_BREADTH, Traversal::defaultMaxBreadth); }
/** 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));
/** We get an iterator over the branching nodes. */
ProgressGraphIterator<BranchingNode,ProgressTimerAndSystem> itBranching (graph.iterator<BranchingNode>(), progressFormat0);
/** We create the Terminator. */
BranchingTerminator terminator (graph);
/** We create the starting node selector according to the user choice. */
INodeSelector* starter = NodeSelectorFactory::singleton().create (getInput()->getStr(STR_STARTER_KIND), graph, terminator);
LOCAL (starter);
/** We create the Traversal instance according to the user choice. */
Traversal* traversal = Traversal::create (
getInput()->getStr(STR_TRAVERSAL_KIND),
graph,
terminator,
getInput()->getInt (STR_CONTIG_MAX_LEN),
getInput()->getInt (STR_BFS_MAX_DEPTH),
getInput()->getInt (STR_BFS_MAX_BREADTH)
);
LOCAL (traversal);
Path consensusRight;
Path consensusLeft;
u_int64_t nbContigs = 0;
u_int64_t nbSmallContigs = 0;
u_int64_t totalNt = 0;
u_int64_t maxContigLen = 0;
u_int64_t maxContigLenLeft = 0;
u_int64_t maxContigLenRight = 0;
bool isNoLengthCutoff = getParser()->saw(STR_NO_LENGTH_CUTOFF);
Sequence seq (Data::ASCII);
/** We loop over the branching nodes. */
for (itBranching.first(); !itBranching.isDone(); itBranching.next())
{
DEBUG ((cout << endl << "-------------------------- " << graph.toString (itBranching.item()) << " -------------------------" << endl));
Node startingNode;
// keep looping while a starting kmer is available from this kmer
// everything will be marked during the traversal()'s
while (starter->select (itBranching.item(), startingNode) == true)
{
/** We compute right and left extensions of the starting node. */
int lenRight = traversal->traverse (startingNode, DIR_OUTCOMING, consensusRight);
int lenLeft = traversal->traverse (graph.reverse(startingNode), DIR_OUTCOMING, consensusLeft);
int lenTotal = graph.getKmerSize() + lenRight + lenLeft;
/** We keep this contig if its size is long enough. */
if (lenTotal >= 2*graph.getKmerSize()+1 || isNoLengthCutoff)
{
/** We create the contig sequence. */
buildSequence (graph, startingNode, lenTotal, nbContigs, consensusRight, consensusLeft, seq);
/** We add the sequence into the output bank. */
outputBank->insert (seq);
nbContigs += 1;
totalNt += lenTotal;
traversal->commit_stats();
if (lenTotal > maxContigLen) { maxContigLen = lenTotal; }
if (lenLeft > maxContigLenLeft) { maxContigLenLeft = lenLeft; }
if (lenRight > maxContigLenRight) { maxContigLenRight = lenRight; }
}
else
{
traversal->revert_stats();
nbSmallContigs++;
}
} /* end of while (starter->select() */
} /* end of for (itBranching.first() */
/** 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", traversal->getName().c_str());
getInfo()->add
6EF2
(2, "start_selector", "%s", starter->getName().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, "max_length_left", "%d", maxContigLenLeft);
getInfo()->add (2, "max_length_right", "%d", maxContigLenRight);
getInfo()->add (2, "debugging traversal stats");
getInfo()->add (2, "large breadth", "%d", traversal->final_stats.couldnt_traverse_bubble_breadth);
getInfo()->add (2, "large depth", "%d", traversal->final_stats.couldnt_traverse_bubble_depth);
getInfo()->add (2, "marked kmer inside traversal", "%d", traversal->final_stats.couldnt_because_marked_kmer);
getInfo()->add (2, "traversal ends with dead-ends", "%d", traversal->final_stats.couldnt_find_extension);
getInfo()->add (2, "in-branching large depth", "%d", traversal->final_stats.couldnt_inbranching_depth);
getInfo()->add (2, "in-branching large breadth", "%d", traversal->final_stats.couldnt_inbranching_breadth);
getInfo()->add (2, "in-branching other", "%d", traversal->final_stats.couldnt_inbranching_other);
getInfo()->add (2, "couldn't validate consensuses", "%d", traversal->final_stats.couldnt_validate_consensuses);
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
void Minia::buildSequence (
const Graph& graph,
const Node& startingNode,
size_t length,
size_t nbContigs,
const Path& consensusRight,
const Path& consensusLeft,
Sequence& seq
)
{
/** Shortcuts. */
Data& data = seq.getData();
size_t lenRight = consensusRight.size();
size_t lenLeft = consensusLeft.size ();
/** We set the sequence comment. */
stringstream ss1;
ss1 << nbContigs << "__len__" << length;
seq._comment = ss1.str();
/** We set the data length. */
seq.getData().resize (length);
size_t idx=0;
/** We dump the left part. */
for (size_t i=0; i<lenLeft; i++) { data[idx++] = ascii (reverse(consensusLeft [lenLeft-i-1])); }
/** We dump the starting node. */
string node = graph.toString (startingNode);
for (size_t i=0; i<node.size(); i++) { data[idx++] = node[i]; }
/** We dump the right part. */
for (size_t i=0; i<lenRight; i++) { data[idx++] = ascii (consensusRight[i]); }
}