1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258
|
#include<fstream>
#include<set>
#include"TranscriptInfo.h"
#include "common.h"
bool TranscriptInfo::writeInfo(string fileName, bool force) const{//{{{
ofstream trF;
if(! force){
// Do nothing if file exists.
ifstream testF(fileName.c_str());
if(testF.is_open()){
testF.close();
return false;
}
testF.close();
}
trF.open(fileName.c_str(),ios::out | ios::trunc);
if(! trF.is_open() ) return false;
trF<<"# M "<<M<<endl;
for(long i=0;i<M;i++)
trF<<transcripts[i].g<<" "<<transcripts[i].t<<" "<<transcripts[i].l<<" "<<transcripts[i].effL<<endl;
trF.close();
return true;
}//}}}
bool TranscriptInfo::writeGeneInfo(string fileName) const{//{{{
ofstream geF;
geF.open(fileName.c_str(),ios::out | ios::trunc);
if(! geF.is_open() ) return false;
geF<<"# G "<<G<<endl;
geF<<"# <gene name> <# of transcripts> <average length>"<<endl;
double length;
for(long i=0;i<G;i++){
length = 0;
for(long j=0;j<genes[i].m;j++)length+=transcripts[genes[i].trs[j]].l;
geF<<genes[i].name<<" "<<genes[i].m<<" "<<length/genes[i].m<<endl;
}
geF.close();
return true;
}//}}}
bool TranscriptInfo::setInfo(vector<string> gNames,vector<string> tNames, vector<long> lengths){//{{{
// The sizes have to be equal.
if((gNames.size()!=tNames.size())||(tNames.size()!=lengths.size())) return false;
transcriptT newT;
M = (long) gNames.size();
// Create new entry for each transcript.
for(long i=0;i<M;i++){
newT.g=gNames[i];
newT.t=tNames[i];
newT.gI = 0;
newT.l=(int_least32_t)lengths[i];
newT.effL = lengths[i];
transcripts.push_back(newT);
}
// Initialize gene info based on gene names.
setGeneInfo();
isInitialized = true;
return isInitialized;
}//}}}
void TranscriptInfo::setGeneInfo(){//{{{
// Cleanup previous gene list.
genes.clear();
// Map of genes: name -> position within gene vector.
map<string,long> names;
geneT tmpG;
long gi=0,i;
groupedByGenes = true;
string previousName = "!-noname-!";
for(i=0;i<M;i++){
// If gene name same as previous, then just add new transcript.
if(transcripts[i].g == previousName){
transcripts[i].gI = gi;
genes[gi].m++;
genes[gi].trs.push_back(i);
}else{
previousName=transcripts[i].g;
// Check whether the gene name is new or was seen before.
if(names.count(transcripts[i].g) == 0){
// Prepare entry for new gene, starting with one (current) transcript.
tmpG.name = transcripts[i].g;
tmpG.m = 1;
tmpG.trs = vector<long>(1,i);
// Add entry to the gene list.
genes.push_back(tmpG);
// Set current gene index.
gi=genes.size()-1;
transcripts[i].gI = gi;
// Map gene name to it's index and update previousName.
names[transcripts[i].g] = gi;
}else{
// If gene name was seen before then transcripts are not grouped by genes.
groupedByGenes=false;
//warning("TranscriptInfo: Transcripts of gene %ld are not grouped.\n",transcripts[i].g);
gi = names[transcripts[i].g];
transcripts[i].gI = gi;
genes[gi].m++;
genes[gi].trs.push_back(i);
}
}
}
G = genes.size();
// Add empty record to the end.
tmpG.name = "";
tmpG.m = 0;
tmpG.trs.clear();
genes.push_back(tmpG);
}//}}}
TranscriptInfo::TranscriptInfo(){ clearTranscriptInfo(); }
void TranscriptInfo::clearTranscriptInfo(){//{{{
M=G=0;
isInitialized=false;
groupedByGenes=true;
transcripts.clear();
genes.clear();
}//}}}
TranscriptInfo::TranscriptInfo(string fileName){//{{{
noName="wrongID";
// TranscriptInfo();
readInfo(fileName);
}//}}}
bool TranscriptInfo::readInfo(string fileName){//{{{
clearTranscriptInfo();
ifstream trFile(fileName.c_str());
if(!trFile.is_open()){
error("TranscriptInfo: problem reading transcript file.\n");
return false;
}
transcriptT newT;
// Read all lines of file ignoring lines starting with #.
while(trFile.good()){
while(trFile.good() && (trFile.peek()=='#'))
trFile.ignore(100000000,'\n');
if(!trFile.good()) break;
// Read gene name, tr name and length.
trFile>>newT.g>>newT.t>>newT.l;
newT.gI = 0;
// Should not hit EOF or any other error yet.
if(!trFile.good()) break;
// Read effective length if present:
while((trFile.peek() == '\t')||(trFile.peek() == ' ')) trFile.get();
// If end of line is reached then use length as effective length.
if((trFile.good()) && (trFile.peek() == '\n')) newT.effL = newT.l;
else trFile>>newT.effL;
// If the line was OK, then push new entry (EOF when looking for effective length is allowed).
if(!trFile.fail())
transcripts.push_back(newT);
// Ignore rest of the line.
trFile.ignore(100000000,'\n');
}
trFile.close();
isInitialized = true;
M = (long)transcripts.size();
setGeneInfo();
return isInitialized;
}//}}}
long TranscriptInfo::getM() const{//{{{
return M;
}//}}}
long TranscriptInfo::getG() const{//{{{
return G;
}//}}}
const vector<long> &TranscriptInfo::getGtrs(long i) const{//{{{
if((i>G) || (i<0)){
// Return empty record.
return genes[G].trs;
}
return genes[i].trs;
}//}}}
double TranscriptInfo::effL(long i) const{//{{{
if(isInitialized && (i<M))return transcripts[i].effL;
return 0;
}//}}}
long TranscriptInfo::L(long i) const{//{{{
if(isInitialized && (i<M))return transcripts[i].l;
return 0;
}//}}}
const string &TranscriptInfo::trName(long i) const{//{{{
if(isInitialized && (i<M))return transcripts[i].t;
return noName;
}//}}}
const string &TranscriptInfo::geName(long i) const{//{{{
if(isInitialized && (i<M))return transcripts[i].g;
return noName;
}//}}}
long TranscriptInfo::geId(long i) const{//{{{
if(isInitialized && (i<M))return transcripts[i].gI;
return -1;
}//}}}
void TranscriptInfo::setEffectiveLength(vector<double> effL){//{{{
if((long)effL.size() != M){
warning("TranscriptInfo: Wrong array size for effective length adjustment.\n");
return;
}
// Adjust effective length to similar scale as normal length
double sumL = 0,sumN = 0,norm;
for(long i=0;i<M;i++){
sumN+=effL[i];
sumL+=transcripts[i].l;
}
// don't normalize
// norm = sumL / sumN;
norm = 1;
for(long i=0;i<M;i++){
transcripts[i].effL = effL[i] * norm;
}
}//}}}
vector<double> *TranscriptInfo::getShiftedLengths(bool effective) const{//{{{
vector<double> *Ls = new vector<double>(M+1);
for(long i=0;i<M;i++){
if(effective)(*Ls)[i+1] = transcripts[i].effL;
else (*Ls)[i+1] = transcripts[i].l;
}
return Ls;
}//}}}
bool TranscriptInfo::updateTrNames(const vector<string> &trList){//{{{
if((long)trList.size() != M)return false;
// Check uniqueness of new names.
set<string> trSet(trList.begin(),trList.end());
if((long)trSet.size() != M)return false;
for(long i=0;i<M;i++){
transcripts[i].t = trList[i];
}
return true;
}//}}}
bool TranscriptInfo::updateGeneNames(const vector<string> &geneList){//{{{
if((long)geneList.size() != M){
warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M);
return false;
}
// Copy gene names in the order they are.
for(long i=0;i<M;i++){
transcripts[i].g = geneList[i];
}
// Initialize gene info.
setGeneInfo();
return true;
}//}}}
bool TranscriptInfo::updateGeneNames(const map<string,string> &trGeneList){//{{{
if((long)trGeneList.size() < M){
warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M);
return false;
}
// Check all transcripts have associated gene name.
for(long i=0;i<M;i++){
if(!trGeneList.count(transcripts[i].t)){
warning("TranscriptInfo: No gene name for transcript [%s].",transcripts[i].t.c_str());
return false;
}
}
// Set gene names.
for(long i=0;i<M;i++){
transcripts[i].g = trGeneList.find(transcripts[i].t)->second;
}
// Initialize gene info.
setGeneInfo();
return true;
}//}}}
|