| 1 |
gpertea |
165 |
// |
| 2 |
|
|
// gtfToFasta.h |
| 3 |
|
|
// TopHat |
| 4 |
|
|
// |
| 5 |
|
|
// Created by Harold Pimentel on 10/26/11. |
| 6 |
|
|
// Copyright 2011 __MyCompanyName__. All rights reserved. |
| 7 |
|
|
// |
| 8 |
|
|
|
| 9 |
|
|
#ifndef GTFToFasta_H |
| 10 |
|
|
#define GTFToFasta_H |
| 11 |
|
|
|
| 12 |
|
|
#ifdef HAVE_CONFIG_H |
| 13 |
|
|
#include <config.h> |
| 14 |
|
|
#endif |
| 15 |
|
|
|
| 16 |
|
|
#include <cassert> |
| 17 |
|
|
#include <cstdlib> |
| 18 |
|
|
#include <cstring> |
| 19 |
|
|
#include <fstream> |
| 20 |
|
|
#include <iostream> |
| 21 |
|
|
#include <map> |
| 22 |
|
|
#include <string> |
| 23 |
|
|
#include <sstream> |
| 24 |
|
|
#include <utility> |
| 25 |
|
|
#include <vector> |
| 26 |
|
|
|
| 27 |
|
|
#include "common.h" |
| 28 |
|
|
#include "gff.h" |
| 29 |
|
|
#include "GFaSeqGet.h" |
| 30 |
|
|
#include "FastaTools.h" |
| 31 |
|
|
|
| 32 |
|
|
std::string get_exonic_sequence(GffObj *p_trans, FastaRecord *rec); |
| 33 |
|
|
|
| 34 |
|
|
class GTFToFasta { |
| 35 |
|
|
public: |
| 36 |
|
|
GTFToFasta(std::string gtf_fname, std::string genome_fname); |
| 37 |
|
|
~GTFToFasta(); |
| 38 |
|
|
void make_transcriptome(std::string out_fname); |
| 39 |
|
|
|
| 40 |
|
|
// for debugging |
| 41 |
|
|
void print_mapping(); |
| 42 |
|
|
private: |
| 43 |
|
|
GffReader gtfReader_; |
| 44 |
|
|
GFaSeqGet genome_fhandle_; |
| 45 |
|
|
|
| 46 |
|
|
std::string gtf_fname_; |
| 47 |
|
|
std::string genome_fname_; |
| 48 |
|
|
|
| 49 |
|
|
FILE* gtf_fhandle_; |
| 50 |
|
|
|
| 51 |
|
|
// "contig" => vector(index_of_gff_obj) |
| 52 |
|
|
// typedef std::map<const char* , std::vector< size_t >* > ContigTransMap; |
| 53 |
|
|
typedef std::map<std::string, std::vector< size_t >* > ContigTransMap; |
| 54 |
|
|
ContigTransMap contigTransMap_; |
| 55 |
|
|
|
| 56 |
|
|
void transcript_map(); |
| 57 |
|
|
|
| 58 |
|
|
GTFToFasta(); // Don't want anyone calling the constructor w/o options |
| 59 |
|
|
}; |
| 60 |
|
|
|
| 61 |
|
|
#endif |
