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#include<algorithm>
#include<fstream>
#include<set>
#include<sstream>
#include "TranscriptSequence.h"
#include "misc.h"
#include "common.h"
// Number of times we randomly probe for old cache record.
// CR: #define WORST_SEARCH_N 10
TranscriptSequence::TranscriptSequence(){//{{{
// CR: srand(time(NULL));
M=0;
cM=0;
gotGeneNames=false;
// CR: useCounter = 0;
}//}}}
TranscriptSequence::TranscriptSequence(string fileName, refFormatT format){//{{{
TranscriptSequence();
readSequence(fileName,format);
}//}}}
bool TranscriptSequence::readSequence(string fileName, refFormatT format){//{{{
fastaF.open(fileName.c_str());
if(!fastaF.is_open()){
error("TranscriptSequence: problem reading transcript file.\n");
return false;
}
trSeqInfoT newTr;
// CR: newTr.lastUse=0;
// CR: newTr.cache=-1;
string trDesc,geneName;
long pos;
istringstream geneDesc;
trNames.clear();
geneNames.clear();
gotGeneNames = true;
// Record trNames only from gencode ref.
gotTrNames = (format == GENCODE);
while(fastaF.good()){
while((fastaF.peek()!='>')&&(fastaF.good()))
fastaF.ignore(1000,'\n');
if(! fastaF.good())break;
// Read description line:
getline(fastaF, trDesc, '\n');
// look for gene name if previous lines had gene name:
if(gotGeneNames){
if(format == GENCODE){
vector<string> lineTokens = ns_misc::tokenize(trDesc,"|");
if(lineTokens.size()>1){
geneNames.push_back(lineTokens[1]);
trNames.push_back(lineTokens[0].substr(1));
}else{
gotGeneNames = false;
gotTrNames = false;
}
}else{ // format == STANDARD
pos=min(trDesc.find("gene:"),trDesc.find("gene="));
if(pos!=(long)string::npos){
geneDesc.clear();
geneDesc.str(trDesc.substr(pos+5));
geneDesc >> geneName;
geneNames.push_back(geneName);
}else{
gotGeneNames = false;
}
}
}
// remember position:
newTr.seek=fastaF.tellg();
trs.push_back(newTr);
}
// Exit if there was an error while reading the file.
if(fastaF.bad()){
error("TranscriptSequence: problem reading file.\n");
return false;
}
M = trs.size();
// Allocate cache for all.
cache.resize(M);
//cache.resize(min(M,(long)TRS_CACHE_MAX));
//cachedTrs.resize(min(M,(long)TRS_CACHE_MAX));
// Clear eof flag from input stream.
fastaF.clear();
return loadSequence();
}//}}}
bool TranscriptSequence::loadSequence(){//{{{
cache.resize(M);
string seqLine;
for(long tr=0;tr<M;tr++){
// Set input stream to transcript's position.
fastaF.seekg(trs[tr].seek);
// Read line by line until reaching EOF or next header line '>'.
while((fastaF.peek()!='>')&&( getline(fastaF,seqLine,'\n').good())){
cache[tr]+=seqLine;
}
if(fastaF.bad()){
error("TranscriptSequence: Failed reading transcript %ld\n",tr);
return false;
}
// Clear flags (just in case).
fastaF.clear();
}
return true;
}//}}}
long TranscriptSequence::getG() const{//{{{
if(!gotGeneNames)return 0;
return (set<string>(geneNames.begin(),geneNames.end())).size();
}//}}}
const string &TranscriptSequence::getTr(long tr) const{//{{{
if((tr<0)||(tr>=M))return noneTr;
// Return pointer to the sequence in cache.
return cache[tr];
/* Used with cacheing. {{{
// Update last use info.
trs[tr].lastUse = useCounter++;
return cache[acquireSequence(tr)];
}}} */
}//}}}
string TranscriptSequence::getSeq(long trI,long start,long l,bool doReverse) const{//{{{
// Return empty string for unknown transcript.
if((trI<0)||(trI>=M))return "";
/* Used with cacheing. {{{
// Update last use info.
trs[tr].lastUse = useCounter++;
// Get position within cache.
long trI = acquireSequence(tr);
}}} */
// If position is not within the sequence, return Ns.
if(start>=(long)cache[trI].size())return string(l,'N');
string ret;
// Copy appropriate sequence, fill up the rest with Ns.
if(start<0){
ret.assign(-start,'N');
ret+=cache[trI].substr(0,l+start);
}else{
ret = cache[trI].substr(start,l);
if(((long)ret.size()) < l)ret.append(l-ret.size(), 'N');
}
if(!doReverse){
return ret;
}else{
// For reverse return reversed string with complemented bases.
reverse(ret.begin(),ret.end());
for(long i=0;i<l;i++)
if((ret[i]=='A')||(ret[i]=='a'))ret[i]='T';
else if((ret[i]=='T')||(ret[i]=='t'))ret[i]='A';
else if((ret[i]=='C')||(ret[i]=='c'))ret[i]='G';
else if((ret[i]=='G')||(ret[i]=='g'))ret[i]='C';
return ret;
}
}//}}}
/* long TranscriptSequence::acquireSequence(long tr){//{{{
// If the sequence is stored in cache then just return it's cache index.
if(trs[tr].cache!=-1)return trs[tr].cache;
long i,newP,j;
// See if cache is full.
if(cM<TRS_CACHE_MAX){
// If cache limit not reached, just add new sequence.
newP=cM;
cM++;
}else{
// If cache is full, look at WORST_SEARCH_N positions and choose the one least used.
newP=rand()%cM;
for(i=0;i<WORST_SEARCH_N;i++){
j=rand()%cM;
if(trs[cachedTrs[newP]].lastUse > trs[cachedTrs[j]].lastUse)newP=j;
}
// "remove" the transcript from position newP from cache.
trs[cachedTrs[newP]].cache=-1;
cache[newP].clear();
}
// Set input stream to transcript's position.
fastaF.seekg(trs[tr].seek);
string seqLine;
// Read line by line until reaching EOF or next header line '>'.
while((fastaF.peek()!='>')&&( getline(fastaF,seqLine,'\n').good())){
cache[newP]+=seqLine;
}
if(fastaF.bad()){
error("TranscriptSequence: Failed reading transcript %ld\n",tr);
return 0;
}
// Clear flags.
fastaF.clear();
// Update cache information.
cachedTrs[newP]=tr;
trs[tr].cache=newP;
// Return transcripts index within cache.
return newP;
}//}}} */
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