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#include <pbdata/Enumerations.h>
#include <pbdata/FASTAReader.hpp>
#include <pbdata/FASTASequence.hpp>
#include <pbdata/NucConversion.hpp>
#include <climits>
#include <cstdlib>
#include <iostream>
#include <string>
#include <vector>
#include <sys/fcntl.h>
#include <sys/mman.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
void FASTAReader::SetFileSize()
{
//
// Seek operation returns the amount seeked forwared in bytes.
// This is the size used to map (which is rounded up by the
// system).
//
fileSize = lseek(fileDes, 0, SEEK_END);
lseek(fileDes, 0, SEEK_SET);
}
void FASTAReader::Init()
{
padding = 0;
fileDes = -1;
fileSize = 0;
endOfReadDelim = '>';
readStartDelim = '>';
doToUpper = false;
convMat = PreserveCase;
computeMD5 = false;
filePtr = NULL;
curPos = 0;
}
FASTAReader::FASTAReader() { Init(); }
FASTAReader::FASTAReader(std::string &fileName)
{
Init(); // initialze defaults.
Init(fileName); // open file.
padding = 0;
endOfReadDelim = '>';
readStartDelim = '>';
}
void FASTAReader::SetSpacePadding(int _padding)
{
assert(_padding >= 0);
padding = _padding;
}
void FASTAReader::SetToUpper()
{
doToUpper = true;
convMat = AllToUpper;
}
//
// Synonym for Init() for consistency.
//
int FASTAReader::Initialize(std::string &seqInName) { return Init(seqInName); }
int FASTAReader::Init(std::string &seqInName, int passive)
{
// Check if file is exist and not empty (length of the file is non-zero)
struct stat st;
if (stat(seqInName.c_str(), &st) != 0) {
std::cerr << "FASTA file " << seqInName << " doesn't exist" << std::endl;
std::exit(EXIT_FAILURE);
}
if (st.st_size == 0) {
std::cerr << "FASTA file " << seqInName << " is empty" << std::endl;
std::exit(EXIT_FAILURE);
}
fileDes = open(seqInName.c_str(), O_RDONLY);
padding = 0;
if (fileDes == -1) {
if (passive) {
return 0;
} else {
std::cout << "Could not open FASTA file " << seqInName << std::endl;
std::exit(EXIT_FAILURE);
}
}
SetFileSize();
filePtr = (char *)mmap(0, fileSize, PROT_READ, MAP_PRIVATE, fileDes, 0);
if (filePtr == MAP_FAILED) {
std::cout << "ERROR, Fail to load FASTA file " << seqInName << " to virtual memory."
<< std::endl;
std::exit(EXIT_FAILURE);
}
curPos = 0;
return 1;
}
void FASTAReader::AdvanceToTitleStart(GenomeLength &p, char delim)
{
while (p < fileSize and filePtr[p] != delim) {
p++;
}
}
void FASTAReader::CheckValidTitleStart(GenomeLength &p, char delim)
{
if (p >= fileSize or filePtr[p] != delim) {
std::cout << "ERROR, FASTA entry must begin with \"" << delim << "\"" << std::endl;
std::exit(EXIT_FAILURE);
}
}
GenomeLength FASTAReader::ReadAllSequencesIntoOne(FASTASequence &seq,
SequenceIndexDatabase<FASTASequence> *seqDBPtr)
{
seq.Free();
GenomeLength p = curPos;
AdvanceToTitleStart(p);
CheckValidTitleStart(p);
ReadTitle(p, seq);
if (seq.title == NULL) {
std::cout << "ERROR, sequence must have a nonempty title." << std::endl;
std::exit(EXIT_FAILURE);
}
if (seqDBPtr != NULL) {
seqDBPtr->growableName.push_back(seq.title);
}
GenomeLength seqLength;
seqLength = fileSize - p;
GenomeLength memorySize = seqLength + padding + 1;
if (memorySize > UINT_MAX) {
std::cout << "ERROR! Reading fasta files greater than 4Gbytes is not supported."
<< std::endl;
std::exit(EXIT_FAILURE);
}
seq.Resize(memorySize);
GenomeLength i;
i = 0L;
for (; p < fileSize; p++, i++) {
seq.seq[i] = filePtr[p];
}
i = p = 0;
while (p < seqLength) {
//
// If this is the beginning of another read, add an 'N'
// to delineate spaces between reads.
//
while (p < seqLength && (seq.seq[p] == ' ' || seq.seq[p] == '\n' || seq.seq[p] == '\t' ||
seq.seq[p] == '\r')) {
p++;
}
if (p < seqLength && seq.seq[p] == '>') {
seq.seq[i] = 'N';
GenomeLength titleStartPos = p + 1;
i++;
while (p < seqLength and seq.seq[p] != '\n')
p++;
if (seqDBPtr != NULL and p < seqLength) {
std::string title;
GenomeLength tp;
for (tp = titleStartPos; tp < p; tp++) {
title.push_back(seq.seq[tp]);
}
seqDBPtr->growableName.push_back(title);
seqDBPtr->growableSeqStartPos.push_back(i);
int nSeq = seqDBPtr->growableSeqStartPos.size();
if (nSeq > 1 and computeMD5) {
std::string md5Str;
MakeMD5((const char *)&seq.seq[seqDBPtr->growableSeqStartPos[nSeq - 2]],
seqDBPtr->growableSeqStartPos[nSeq - 1] -
seqDBPtr->growableSeqStartPos[nSeq - 2] - 1,
md5Str);
seqDBPtr->md5.push_back(md5Str);
}
}
} else if (p < seqLength) {
// Otherwise, p may be at whitespace
// advance past that as well.
seq.seq[i] = convMat[seq.seq[p]];
i++;
p++;
}
}
if (i > UINT_MAX) {
std::cout << "ERROR! Sequences greater than 4Gbase are not supported." << std::endl;
std::exit(EXIT_FAILURE);
}
//
// Append an 'N' at the end of the last sequence for consistency
// between different orderings of reference input.
//
seq.seq[i] = 'N';
i++;
seq.length = i;
// fill padding.
for (; i < memorySize; i++) {
seq.seq[i] = 0;
}
seq.deleteOnExit = true;
if (seqDBPtr != NULL) {
seqDBPtr->growableSeqStartPos.push_back(seq.length);
int nSeq = seqDBPtr->growableSeqStartPos.size();
if (nSeq > 1 and computeMD5) {
std::string md5Str;
MakeMD5((const char *)&seq.seq[seqDBPtr->growableSeqStartPos[nSeq - 2]],
seqDBPtr->growableSeqStartPos[nSeq - 1] -
seqDBPtr->growableSeqStartPos[nSeq - 2] - 1,
md5Str);
seqDBPtr->md5.push_back(md5Str);
}
seqDBPtr->Finalize();
}
return seq.length;
}
void FASTAReader::ReadTitle(GenomeLength &p, FASTASequence &seq)
{
char *seqTitle = NULL;
int seqTitleLen;
ReadTitle(p, seqTitle, seqTitleLen);
seq.CopyTitle(seqTitle, seqTitleLen);
if (seqTitle) {
delete[] seqTitle;
}
}
void FASTAReader::ReadTitle(GenomeLength &p, char *&title, int &titleLength)
{
//
// Extract the title. The length of the title does not include the newline.
//
p++; // Move past '>'
curPos = p;
while (p < fileSize and filePtr[p] != '\n') {
p++;
}
titleLength = p - curPos;
if (titleLength > 0) {
if (title) {
delete[] title;
title = NULL;
}
title = ProtectedNew<char>(titleLength + 1);
if (title == nullptr) {
std::cout << "ERROR, unable to read FASTA file to memory. " << std::endl;
std::exit(EXIT_FAILURE);
}
int t = 0;
for (p = curPos; p < curPos + titleLength; p++, t++) {
title[t] = filePtr[p];
}
title[titleLength] = '\0';
} else {
title = NULL;
titleLength = 0;
}
}
int FASTAReader::GetNext(FASTASequence &seq)
{
if (curPos == fileSize) {
return 0;
}
seq.Free(); //Free seq before read
//
// Extract the title of the current record.
//
GenomeLength p = curPos;
AdvanceToTitleStart(p);
//
// Make sure there is a '>'
//
CheckValidTitleStart(p);
ReadTitle(p, seq);
//
// Read in the next sequence.
//
// Count the length of the sequence.
GenomeLength seqLength = 0;
curPos = p;
char c;
while (p < fileSize and (c = filePtr[p]) != endOfReadDelim) {
if (c != ' ' and c != '\t' and c != '\n' and c != '\r') {
seqLength++;
}
p++;
}
if (seqLength > UINT_MAX) {
std::cout
<< "ERROR! Reading sequences stored in more than 4Gbytes of space is not supported."
<< std::endl;
std::exit(EXIT_FAILURE);
}
seq.length = 0;
if (seqLength > 0) {
seq.length = seqLength;
seq.seq = ProtectedNew<Nucleotide>(seqLength + padding + 1);
p = curPos;
seq.deleteOnExit = true;
GenomeLength s = 0;
while (p < fileSize and (c = filePtr[p]) != endOfReadDelim) {
if (c != ' ' and c != '\t' and c != '\n' and c != '\r') {
seq.seq[s] = convMat[static_cast<unsigned char>(filePtr[p])];
s++;
}
p++;
}
seq.seq[seqLength] = 0;
}
curPos = p;
if (computeMD5) {
MakeMD5((const char *)&seq.seq, seq.length, curReadMD5);
}
return 1;
}
/*
Advance to the read nSeq forward.
input: nSeq, the number of sequences to skip.
output:
returns 1 if after advancing nSeq sequences, the file pointer is pointing to
a new sequence.
0 otherwise.
A return value of 0 will signal that the file is done being processed if it is
iterting over reads.
*/
int FASTAReader::Advance(int nSeq)
{
int nAdvanced = 0;
GenomeLength p = curPos;
// base case -- it's always ok to advance 0
if (nSeq == 0) {
return 1;
}
// Make sure the advance starts at
// the beginning of a sequence.
while (p < fileSize and filePtr[p] != endOfReadDelim)
p++;
// No sequence was found, coudln't advance.
if (p >= fileSize) {
return 0;
}
p++;
nAdvanced = 1;
while (nAdvanced <= nSeq and p < fileSize) {
if (filePtr[p] == endOfReadDelim) {
if (nAdvanced == nSeq) {
//
// Want to end with the reader on a '>', so return before
// hitting the rest of the loop.
//
curPos = p;
return 1;
} else {
nAdvanced++;
}
}
p++;
}
curPos = p;
return 0;
}
int FASTAReader::CriticalGetNext(FASTASequence &seq)
{
if (!GetNext(seq)) {
std::cout << "Could not read a sequence." << std::endl;
std::exit(EXIT_FAILURE);
}
return 1;
}
int FASTAReader::ConcatenateNext(FASTASequence &cur)
{
FASTASequence next;
int retVal;
if ((retVal = GetNext(next))) {
next.CleanupASCII();
cur.Concatenate((Nucleotide *)"N");
cur.Concatenate(next);
}
next.Free();
return retVal;
}
void FASTAReader::Close()
{
if (fileDes == -1) {
std::cout << "ERROR, calling close on an uninitialized fasta reader" << std::endl;
std::exit(EXIT_FAILURE);
} else {
munmap(filePtr, fileSize);
close(fileDes);
fileDes = -1;
}
}
void FASTAReader::ReadAllSequences(std::vector<FASTASequence> &sequences)
{
//
// Step 1, compute the number of reads in the file.
//
GenomeLength p;
p = 0;
int nSeq = 0;
while (p < fileSize) {
if (filePtr[p] == '>') {
++nSeq;
}
p++;
}
p = 0;
sequences.resize(nSeq);
int curSeq = 0;
while (GetNext(sequences[curSeq])) {
++curSeq;
}
}
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