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#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSequence.h"
#include "libGenome/gnGBKSource.h"
#include "libGenome/gnFASSource.h"
#include <algorithm>
static boolean LocationLessthan(const gnLocation& a, const gnLocation& b);
static boolean LocationLessthan(const gnLocation& a, const gnLocation& b){
return a.GetStart() < b.GetStart();
}
static boolean LocationEndLessthan(const gnLocation& a, const gnLocation& b);
static boolean LocationEndLessthan(const gnLocation& a, const gnLocation& b){
return a.GetEnd() < b.GetStart();
}
static boolean LocationSizeLessthan(const gnLocation& a, const gnLocation& b);
static boolean LocationSizeLessthan(const gnLocation& a, const gnLocation& b){
return a.GetEnd() - a.GetStart() < b.GetEnd() - b.GetStart();
}
// create a location list which contains every intervening region
// in l_list
void ComplementLocation(vector<gnLocation>& l_list){
if(l_list.size() < 2)
return; //need 2 or more locations to get the in between regions
vector<gnLocation> comp_list;
sort(l_list.begin(), l_list.end(), &LocationLessthan);
for(uint32 locationI = 1; locationI < l_list.size(); locationI++){
//if they don't intersect there is an intervening region
if( !l_list[locationI].Intersects( l_list[locationI-1] ) ){
//create the region between locationI and locationI - 1
gnLocation between_loc;
between_loc.SetStart(l_list[locationI-1].GetEnd());
between_loc.SetEnd(l_list[locationI].GetStart());
//add it to the complement list
comp_list.push_back(between_loc);
}
}
l_list = comp_list;
}
void DeleteRepeats(list<gnLocation>& loc_list){
loc_list.sort(&LocationLessthan);
list<gnLocation>::iterator loc_iter = loc_list.begin();
list<gnLocation>::iterator cur_loc;
for(; loc_iter != loc_list.end(); loc_iter++){
cur_loc = loc_iter;
cur_loc++;
while(cur_loc != loc_list.end() && !LocationEndLessthan(*loc_iter, *cur_loc)){
if(loc_iter->Intersects(*cur_loc)){
*loc_iter = loc_iter->GetUnion(*cur_loc);
list<gnLocation>::iterator to_del = cur_loc;
cur_loc--;
loc_list.erase(to_del);
}
cur_loc++;
}
}
}
void WriteData(gnSequence& file_sequence, list<gnLocation>& loc_list, string& filename){
gnSequence loc_seq;
cout << "Gathering sequence data to write...\n";
list<gnLocation>::iterator loc_iter = loc_list.begin();
uint32 loc_count = loc_list.size();
uint32 notice_interval = loc_count / 10;
uint32 cur_locI = 0;
for(;loc_iter != loc_list.end(); loc_iter++){
loc_seq += file_sequence.ToString( loc_iter->GetEnd() - loc_iter->GetStart(), loc_iter->GetStart());
if(cur_locI % notice_interval == 0){
cout << (cur_locI / loc_count) * 10 << "%..";
}
cur_locI++;
}
cout << "\nWriting sequence data...\n";
gnFASSource::Write(loc_seq, filename);
}
void WriteList(list<gnLocation>& loc_list, string& filename){
ofstream list_out(filename.c_str());
list<gnLocation>::iterator loc_iter = loc_list.begin();
for(;loc_iter != loc_list.end(); loc_iter++){
list_out << loc_iter->GetStart() << '\t' << loc_iter->GetEnd() << '\n';
}
list_out.close();
}
void print_usage(char* pname){
cout << "Usage: " << pname << " <genbank file> <exon_list> <intron_list> <exon_seq> <intron_seq>\n";
}
int main( int argc, char* argv[] )
{
boolean run_interactive = false;
string seq_filename;
string exon_list_filename;
string intron_list_filename;
string exon_seq_filename;
string intron_seq_filename;
// define a gnSequence to store the sequence
gnSequence file_sequence;
if(!run_interactive){
// check for correct calling semantics
if(argc != 6){
print_usage(argv[0]);
return -1;
}
seq_filename = argv[1];
exon_list_filename = argv[2];
intron_list_filename = argv[3];
exon_seq_filename = argv[4];
intron_seq_filename = argv[5];
}else{
// Get the name of the sequence to load
cout << "Enter the name of the sequence file to load:\n" ;
cin >> seq_filename;
}
// Load the sequence and tell the user if it loaded successfully
if(file_sequence.LoadSource(seq_filename))
{
cout << seq_filename << " loaded successfully. " << file_sequence.length() << " base pairs.\n";
}else{
cout << "Error loading file.\n";
return -1;
}
uint32 feature_count = file_sequence.getFeatureListLength();
uint32 cds_count = 0;
//define a sequence for each type of data
gnSequence exon_seq;
gnSequence intron_seq;
list<gnLocation> exon_list;
list<gnLocation> intron_list;
cout << "There are " << feature_count << " known features.\n";
for(uint32 featureI = 0; featureI < feature_count; featureI++){
gnBaseFeature* cur_feat = file_sequence.getFeature(featureI);
if(cur_feat == NULL){
cout << "cur_feat is NULL, trace me!\n";
cur_feat = file_sequence.getFeature(featureI);
continue;
}
if(cur_feat->GetName() == "CDS"){
cds_count++;
uint32 loc_count = cur_feat->GetLocationListLength();
vector<gnLocation> cur_exon_list, cur_intron_list;
for(uint32 locationI = 0; locationI < loc_count; locationI++){
cur_exon_list.push_back(cur_feat->GetLocation(locationI));
exon_list.push_back(cur_exon_list[locationI]);
}
if(loc_count >= 2){
cur_intron_list = cur_exon_list;
ComplementLocation(cur_intron_list);
for(uint32 locationI = 0; locationI < cur_intron_list.size(); locationI++)
intron_list.push_back(cur_intron_list[locationI]);
}
/* Code for exon size tracking */
/* sort(cur_exon_list.begin(), cur_exon_list.end(), &LocationSizeLessthan);
gnSeqI cur_size = cur_exon_list[loc_count - 1].GetEnd() - cur_exon_list[loc_count - 1].GetStart();
size_out << cur_size << '\n';
if(cur_size > 5000){
cout << "psycho bob is at it again\n";
cout << "Found " << cur_size << " length exon in feature: " << cur_feat->GetName() << "\n";
cout << "Feature Index: " << featureI << "\n";
for(uint32 i=0; i < cur_feat->GetQualifierListLength(); i++){
cout << cur_feat->GetQualifierName(i) << "\t" << cur_feat->GetQualifierValue(i) << "\n";
}
cout << "\n";
} */
delete cur_feat;
}
}
cout << "There are " << cds_count << " cds features.\n";
//now sort the lists and delete repeats and fix overlaps
uint32 exon_count = exon_list.size();
cout << "Deleting exon repeats... ";
DeleteRepeats(exon_list);
cout << "Eliminated " << exon_count - exon_list.size() << " repeats for a total of ";
cout << exon_list.size() << " repeats\n";
uint32 intron_count = intron_list.size();
cout << "Deleting intron repeats... ";
DeleteRepeats(intron_list);
cout << "Eliminated " << intron_count - intron_list.size() << " repeats for a total of ";
cout << intron_list.size() << " repeats\n";
WriteList(exon_list, exon_list_filename);
WriteList(intron_list, intron_list_filename);
WriteData(file_sequence, exon_list, exon_seq_filename);
WriteData(file_sequence, intron_list, intron_seq_filename);
if(run_interactive)
cin >> seq_filename;
return 0;
};
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