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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 <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <list>
#include <utility>
#include "debug.h"
#include "NGraph.h"
#include "Utils.h"
#include "CycleCompression.h"
#define MAX 1024
//MAX2 and MIN2 never used? TODO: Remove?
#define MAX2(a,b) ((a) > (b) ? (a) : (b))
#define MIN2(a,b) ((a) < (b) ? (a) : (b))
using namespace std;
idx_dir reverse_dir(idx_dir node)
{
return make_pair(node.first, reverse_dir(node.second));
}
bool is_same_node( const idx_dir u, const idx_dir v)
{
return (v.first == u.first && v.second == u.second);
}
/*!
* \brief Merge sequence information between two nodes and print it in the snp file
* with bbc number, cycle and length of upper and lower path.
* Returns the merged sequence
* \param seq1 sequence of the upper path
* \param seq2 sequence of the lower path
* \param snp_log_file the file to be printing the two paths
* \param bccid id of the bi-connected component being treated
*/
string merge_sequences( const string seq1, const string seq2 )
{
string merged;
for (int i = 0 ; i < (int)seq1.size(); i++)
merged += (seq1[i] == seq2[i] ? seq1[i] : 'N');
return merged;
}
void output_sequences( string seq1, string seq2, FILE * snp_log_file, const int bccid, const int cycleNum, const int contextL, const int contextR, const int kValue)
{
int u_len = (int)seq1.size();
int l_len = (int)seq2.size();
if( contextL != 0 || contextR !=0 )
{
seq1 = toLowerContext(seq1, contextL, contextR);
seq2 = toLowerContext(seq2, contextL, contextR);
}
if (u_len- (contextL + contextR) > 2* kValue +1) // multiple SNP
{
fprintf(snp_log_file, ">bcc_%d|Cycle_%d|Type_0b|upper_path_Length_%d\n", bccid, cycleNum, u_len- (contextL + contextR));
fprintf(snp_log_file, "%s\n", seq1.c_str());
fprintf(snp_log_file, ">bcc_%d|Cycle_%d|Type_0b|lower_path_Length_%d\n", bccid, cycleNum, l_len- (contextL + contextR));
fprintf(snp_log_file, "%s\n", seq2.c_str());
}
else // single SNP
{
fprintf(snp_log_file, ">bcc_%d|Cycle_%d|Type_0a|upper_path_Length_%d\n", bccid, cycleNum, u_len- (contextL + contextR));
fprintf(snp_log_file, "%s\n", seq1.c_str());
fprintf(snp_log_file, ">bcc_%d|Cycle_%d|Type_0a|lower_path_Length_%d\n", bccid, cycleNum, l_len- (contextL + contextR));
fprintf(snp_log_file, "%s\n", seq2.c_str());
}
}
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