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/* ***************************************************************************
*
* KisSplice
* de-novo calling alternative splicing events from RNA-seq data.
*
* ***************************************************************************
*
* Copyright INRIA
* contributors : Vincent Lacroix
* Pierre Peterlongo
* Gustavo Sacomoto
* Vincent Miele
* Alice Julien-Laferriere
* David Parsons
*
* pierre.peterlongo@inria.fr
* vincent.lacroix@univ-lyon1.fr
*
* This software is a computer program whose purpose is to detect alternative
* splicing events from RNA-seq data.
*
* This software is governed by the CeCILL license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL license and that you accept its terms.
*/
// ===========================================================================
// Include Libraries
// ===========================================================================
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <vector>
#include <memory>
// ===========================================================================
// Include Project Files
// ===========================================================================
#include "debug.h"
#include "NGraph.h"
#include "CGraph.h"
#include "CycleCompression.h"
#include "SplitBcc.h"
#include "Utils.h"
// ===========================================================================
// Define Miscellaneous Functions
// ===========================================================================
void read_edges_and_nodes( char* edges_fname, char* nodes_fname, const int k,
vector<LabelledCEdge>& allEdges, vector<char*>& seqs )
{
File edge_file = File::open_path(edges_fname, "r");
File node_file = File::open_path(nodes_fname, "r");
read_edge_file( edge_file.get_ptr(), allEdges );
read_node_file( node_file.get_ptr(), seqs, k );
}
int main( int argc, char** argv )
{
const char* base_name = "./bcc/graph";
bool output_context = false;
if (argc < 4) {
fprintf( stderr, "Wrong number of arguments!\n" );
fprintf( stderr, "Usage: ./run_modules edge_file node_file k_value path_to_output [--output-context]\n" );
return EXIT_SUCCESS;
}
if (argc >= 5) {
base_name = argv[4];
}
if ( argc == 6 && strcmp(argv[5], "--output-context") == 0 )
{
output_context = true;
}
const int k_value = atoi( argv[3] );
// Read input files
std::vector<char*> seqs;
std::vector<LabelledCEdge> allEdges;
read_edges_and_nodes( argv[1], argv[2], k_value, allEdges, seqs );
// Creating & Initializing the graph with the edges reads
CGraph graph {(int)seqs.size(), allEdges, k_value};
// Decompose graph into BCCs
fprintf(stdout, "Searching biconnected components...\n");
std::vector<std::vector<CEdge>> bcc = find_bcc(graph);
fprintf(stdout, "Number of biconnected components found: %zu\n\n", bcc.size());
graph.destroy_adj_list();
// P1 - descriptor files
File contents_edge_file = File::open_path_sprintf("%s_contents_edges_bcc", "w", base_name);
File contents_node_file = File::open_path_sprintf("%s_contents_nodes_bcc", "w", base_name);
int lines_written_edges = 0;
int lines_written_nodes = 0;
contents_edge_file.fprintf("%d\n", lines_written_edges);
contents_node_file.fprintf("%d\n", lines_written_nodes);
// P2 - data files
// Optimization : write one bcc data per file, unless this would exceed NUMBEROFFILES in which case multiple are written per file.
// FIXME find a less convoluted way to deal with that
int output_bcc_file_count;
int records_per_bcc_file;
if (bcc.size() == 0) {
std::fprintf(stderr, "Warning: No BCC to handle, stopping\n");
return EXIT_FAILURE;
} else if (bcc.size() == 1) {
output_bcc_file_count = 1;
records_per_bcc_file = 1;
} else {
output_bcc_file_count = std::min(static_cast<int>(bcc.size()), NUMBEROFFILES);
records_per_bcc_file = (int)bcc.size() / (output_bcc_file_count-1); // this division may have a remainder, then extra file (+1) required
}
int current_bcc_file_id = 0;
File current_total_edge_file = File::open_path_sprintf("%s_all_edges_bcc_%d", "w", base_name, current_bcc_file_id+1);
File current_total_node_file = File::open_path_sprintf("%s_all_nodes_bcc_%d", "w", base_name, current_bcc_file_id+1);
File total_log_file = File::open_path_sprintf("%s_all_log_bcc", "w", base_name);
File info_snp_file = File::open_path_sprintf("%s_info_snp_bcc", "w", base_name);
// P3 - ascii info file to get all parameters to read the big files
File info_file = File::open_path_sprintf("%s_info_bcc", "w", base_name);
info_file.fprintf("%zu\n", bcc.size());
info_file.fprintf("%d\n", records_per_bcc_file);
// For each BCC, ...
for ( int i = 0 ; i < (int)bcc.size() ; i++ )
{
fprintf(stdout, "Processing component %d...\n", i+1);
// Build uncompact graph corresponding to current BCC
auto component = NGraph(graph, seqs, allEdges, bcc[i]);
fprintf(stdout, "Initial size: %d nodes.\n", component.getNbNodes() );
// Compress linear paths of size > 2
fprintf(stdout, "Compressing linear paths...\n");
int original_size = component.getNbNodes();
component.compress_all_paths();
fprintf( stdout, "Number of compressed nodes: %d.\n", original_size - component.getNbNodes() );
// Compress bubbles
fprintf( stdout, "Compressing simple bubbles...\n" );
int n_compressed_bubbles = 0;
component.compress_all_bubbles( &n_compressed_bubbles, total_log_file.get_ptr(), i+1, output_context );
fprintf( stdout, "Number of compressed bubbles: %d.\n", n_compressed_bubbles );
int nbsnps = component.getNbOutput();
if (nbsnps) {
info_snp_file.fprintf("%d\t%d\n", i+1, nbsnps); // considering (i+1) and not i
}
// Recompress linear paths of size > 2
fprintf(stdout, "Recompressing linear paths...\n");
original_size = component.getNbNodes();
component.compress_all_paths();
fprintf( stdout, "Number of compressed nodes: %d.\n", original_size - component.getNbNodes() );
if (component.getNbNodes() >= 4) {
// IO optimization
component.print_graph_edges_new( &lines_written_edges, contents_edge_file.get_ptr(),current_total_edge_file.get_ptr(), NULL, NULL, false );
component.print_graph_nodes_new( &lines_written_nodes, contents_node_file.get_ptr(),current_total_node_file.get_ptr(), NULL, NULL, false );
} else {
contents_edge_file.fprintf("%d\n", lines_written_edges);
contents_node_file.fprintf("%d\n", lines_written_nodes);
}
fprintf(stdout, "Final size: %d nodes.\n", component.getNbNodes());
info_file.fprintf("%d %d\n", i+1, component.getNbNodes()); // outuput size of bcc for further use
fprintf(stdout, "Done!\n\n");
// IO optimization: check if output bcc file has to be changed - considering (i+1) and not i
if (((i+1) % records_per_bcc_file == 0) && ((current_bcc_file_id+1) < output_bcc_file_count)) {
current_bcc_file_id += 1;
current_total_edge_file = File::open_path_sprintf("%s_all_edges_bcc_%d", "w", base_name, current_bcc_file_id+1);
current_total_node_file = File::open_path_sprintf("%s_all_nodes_bcc_%d", "w", base_name, current_bcc_file_id+1);
lines_written_edges = 0;
lines_written_nodes = 0;
//write an additional 0 in the first place
contents_edge_file.fprintf("%d\n", lines_written_edges);
contents_node_file.fprintf("%d\n", lines_written_nodes);
}
}
for (char* seq : seqs) {
delete[] seq;
}
return EXIT_SUCCESS;
}
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