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#include <sstream>
#include <pbdata/FASTAReader.hpp>
#include <pbdata/FASTASequence.hpp>
#include <pbdata/utils.hpp>
int main(int argc, char* argv[])
{
std::string seqInName, seqOutName, dotOutName;
if (argc < 4) {
std::cout << "usage: exciseRepeats inName repMaskOutFile outName" << std::endl;
std::exit(EXIT_FAILURE);
}
seqInName = argv[1];
dotOutName = argv[2];
seqOutName = argv[3];
FASTAReader reader;
reader.Initialize(seqInName);
FASTASequence origSeq;
reader.GetNext(origSeq);
std::ifstream dotOutFile;
CrucialOpen(dotOutName, dotOutFile);
std::ofstream seqOutFile;
std::ofstream seqOut;
CrucialOpen(seqOutName, seqOut, std::ios::out);
std::string dotOutLine;
getline(dotOutFile, dotOutLine);
getline(dotOutFile, dotOutLine);
getline(dotOutFile, dotOutLine);
while (getline(dotOutFile, dotOutLine)) {
std::stringstream lineStrm(dotOutLine);
int swScore;
float pctDiv, pctDel, pctIns;
std::string query;
DNALength qPosBegin, qPosEnd;
std::string left;
char strand;
std::string matchingRepeat;
std::string repClass;
std::string repPos, repEnd, repLeft;
int id;
lineStrm >> swScore >> pctDiv >> pctDel >> pctIns >> query >> qPosBegin >> qPosEnd >>
left >> strand >> matchingRepeat >> repClass >> repPos >> repEnd >> repLeft >> id;
for (DNALength seqPos = qPosBegin; seqPos < qPosEnd; seqPos++) {
origSeq.seq[seqPos] = 'X';
}
}
DNALength seqPos, unexPos;
unexPos = 0;
for (seqPos = 0; seqPos < origSeq.length; seqPos++) {
if (origSeq.seq[seqPos] != 'X') {
origSeq.seq[unexPos] = origSeq.seq[seqPos];
unexPos++;
}
}
origSeq.length = unexPos;
origSeq.PrintSeq(seqOut);
return 0;
}
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