int main(int argc, char* argv[]) {
string genomeFileName, subseqFileName;
if (argc != 3) {
cout << "usage: extractRepeats genome repeat" << endl;
exit(0);
}
genomeFileName = argv[1];
subseqFileName = argv[2];
FASTASequence genome, sub;
FASTAReader reader;
reader.Init(genomeFileName);
reader.GetNext(genome);
reader.Init(subseqFileName);
reader.GetNext(sub);
genome.ToUpper();
sub.ToUpper();
DNALength genomePos;
FASTASequence genomeSub;
int kband = (int) (0.15) * sub.length;
vector<int> scoreMat;
vector<Arrow> pathMat;
int readIndex = 0;
cout << "starting extraction" << endl;
for (genomePos = 0; genomePos < genome.length - sub.length + 1; genomePos++) {
genomeSub.seq = &genome.seq[genomePos];
genomeSub.length = sub.length;
int alignScore;
Alignment alignment;
alignScore = SWAlign(genomeSub, sub,
EditDistanceMatrix, 1, //1,kband,
scoreMat, pathMat,
alignment, QueryFit);
if (alignScore < 0.25 * sub.length) {
stringstream titlestrm;
titlestrm << readIndex << "|"
<< genomePos << "|"
<< genomePos + sub.length << " " << alignScore/ (1.0*sub.length);
FASTASequence subcopy;
subcopy.CopyTitle(titlestrm.str());
subcopy.seq = &genome.seq[genomePos];
subcopy.length = sub.length;
subcopy.PrintSeq(std::cout);
genomePos += sub.length;
}
}
}
int main(int argc, char* argv[]) {
if (argc < 3) {
cout << "usage: testBuildOccBins genomeFileName suffixArray" << endl;
exit(0);
}
string genomeFileName = argv[1];
string suffixArrayFileName = argv[2];
FASTAReader reader;
reader.Init(genomeFileName);
FASTASequence seq;
reader.GetNext(seq);
DNASuffixArray suffixArray;
suffixArray.Read(suffixArrayFileName);
Bwt<PackedDNASequence, FASTASequence> bwt;
//bwt.InitializeFromSuffixArray(seq, suffixArray.index);
bwt.InitializeBWTStringFromSuffixArray(seq, suffixArray.index);
bwt.occ.Initialize(bwt.bwtSequence, 4096, 64);
bwt.occ.PrintBins(cout);
}
int main(int argc, char* argv[]) {
string seqFileName;
TupleMetrics tm;
string outFileName;
if (argc < 3) {
cout << "usage: storeTuplePosList seqFile tupleSize outFile" << endl;
return 0;
}
seqFileName = argv[1];
tm.tupleSize = atoi(argv[2]);
outFileName = argv[3];
ofstream outFile;
// CrucialOpen(outFileName, outFile, std::ios::out| std::ios::binary);
FASTAReader reader;
reader.Init(seqFileName);
FASTASequence seq;
reader.GetNext(seq);
// vector<PositionDNATuple>
TupleList<PositionDNATuple>tuplePosList;
tuplePosList.SetTupleMetrics(tm);
// StoreTuplePosList(seq, tm, tuplePosList);
SequenceToTupleList(seq, tm, tuplePosList);
tuplePosList.Sort();
tuplePosList.WriteToFile(outFileName); //WriteTuplePosList(tuplePosList, tm.tupleSize, outFile);
outFile.close();
return 0;
}
int main(int argc, char* argv[]) {
if (argc < 3) {
cout << "usage: bwtLocateList bwtName querySeqFile" << endl;
exit(1);
}
string bwtFileName = argv[1];
string querySeqFileName = argv[2];
bool doPrintResults = false;
int maxCount = 0;
int argi = 3;
bool countOnly = false;
while(argi < argc) {
if (strcmp(argv[argi], "-print") == 0) {
doPrintResults = true;
}
else if (strcmp(argv[argi], "-max") == 0) {
maxCount = atoi(argv[++argi]);
}
else if (strcmp(argv[argi], "-count") == 0) {
countOnly = true;
}
else {
cout << "bad option: " << argv[argi] << endl;
}
++argi;
}
Bwt<PackedDNASequence, FASTASequence> bwt;
bwt.Read(bwtFileName);
FASTAReader queryReader;
queryReader.Init(querySeqFileName);
FASTASequence seq;
int seqIndex = 0;
vector<DNALength> positions;
while(queryReader.GetNext(seq)) {
positions.clear();
if (countOnly == false) {
bwt.Locate(seq, positions, maxCount);
}
else {
DNALength sp,ep;
bwt.Count(seq, sp, ep);
}
// cout << "matched " << positions.size() << " positions." << endl;
if (doPrintResults) {
int i;
for (i = 0; i < positions.size(); i++ ){
cout << positions[i] << " ";
}
cout << endl;
}
++seqIndex;
}
// float wordCountsPerLookup = (bwt.bwtSequence.nCountInWord *1.0) / bwt.bwtSequence.nCountNuc;
// cout << "word counts per lookup: " << wordCountsPerLookup << endl;
return 0;
}
int main(int argc, char *argv[]) {
string sequencesInName, sequencesOutName;
if (argc <3){
cout << "usage: scramble in out" << endl;
exit(1);
}
sequencesInName = argv[1];
sequencesOutName= argv[2];
vector<FASTASequence*> sequences;
vector<int> sequenceIndices;
FASTAReader reader;
reader.Init(sequencesInName);
ofstream out;
CrucialOpen(sequencesOutName, out, std::ios::out);
FASTASequence read;
FASTASequence*readPtr;
while(reader.GetNext(read)) {
readPtr = new FASTASequence;
*readPtr = read;
sequences.push_back(readPtr);
}
int i;
for (i = 0; i < sequences.size(); i++) {
sequenceIndices.push_back(i);
}
for (i = 0; i < 10*sequences.size(); i++ ){
//
// shuffle indices.
//
int idx1;
int idx2;
idx1 = RandomInt(sequences.size());
idx2 = RandomInt(sequences.size());
int tmp;
tmp = sequenceIndices[idx1];
sequenceIndices[idx1] = sequenceIndices[idx2];
sequenceIndices[idx2] = tmp;
}
for (i = 0; i < sequenceIndices.size(); i++ ){
sequences[sequenceIndices[i]]->PrintSeq(out);
}
return 0;
}
int main(int argc, char* argv[]) {
CommandLineParser clp;
string fastaFileName, indexFileName;
vector<string> fastaFileNames;
vector<string> opts;
clp.SetProgramName("bsdb");
clp.SetProgramSummary("Build an index database on a file of sequences.\n"
" The index is used to map to reads given alignment positions.\n");
clp.RegisterStringOption("fasta", &fastaFileName, "A file with sequences to build an index.");
clp.RegisterStringOption("index", &indexFileName, "The index file.");
clp.RegisterPreviousFlagsAsHidden();
clp.ParseCommandLine(argc, argv, opts);
ifstream fastaIn;
ofstream indexOut;
if (FileOfFileNames::IsFOFN(fastaFileName)) {
FileOfFileNames::FOFNToList(fastaFileName, fastaFileNames);
}
else {
fastaFileNames.push_back(fastaFileName);
}
CrucialOpen(indexFileName, indexOut, std::ios::out | std::ios::binary);
SequenceIndexDatabase<FASTASequence> seqDB;
int fileNameIndex;
for (fileNameIndex = 0; fileNameIndex < fastaFileNames.size(); fileNameIndex++){
FASTAReader reader;
FASTASequence seq;
reader.Init(fastaFileNames[fileNameIndex]);
int i = 0;
while (reader.GetNext(seq)) {
seqDB.AddSequence(seq);
i++;
}
}
seqDB.Finalize();
seqDB.WriteDatabase(indexOut);
return 0;
}
int main(int argc, char* argv[]) {
if (argc < 4) {
cout << "usage: splitContigs in.fa contiglength out" << endl;
exit(1);
}
string inFileName, outFileName;
inFileName = argv[1];
int contigLength = atoi(argv[2]);
outFileName = argv[3];
ofstream seqOut;
CrucialOpen(outFileName, seqOut, std::ios::out);
FASTAReader reader;
reader.Init(inFileName);
FASTASequence seq;
DNALength curOffset;
while(reader.GetNext(seq)) {
FASTASequence subseq;
int i;
curOffset = 0;
for (i =0 ; i < seq.length / contigLength + 1; i++ ) {
subseq.seq = &seq.seq[curOffset];
subseq.title = seq.title;
if (curOffset + contigLength > seq.length) {
subseq.length = seq.length - curOffset;
}
else {
subseq.length = contigLength;
}
subseq.PrintSeq(seqOut);
curOffset += contigLength;
}
}
return 0;
}
int main(int argc, char* argv[]) {
string ad1File, ad2File, readsFile, readsOutFile;
FASTAReader ad1Reader;
FASTAReader ad2Reader;
FASTAReader reader;
CommandLineParser cl;
float minPctSimilarity = 0.60;
int indel = 3;
int minLength = 10;
cl.RegisterStringOption("ad1", &ad1File, "FASTA file with the first adapter");
cl.RegisterStringOption("ad2", &ad2File, "FASTA file with the second adapter");
cl.RegisterStringOption("reads", &readsFile, "FASTA file with SMRTBell reads");
cl.RegisterStringOption("readsout", &readsOutFile, "output file for split reads");
cl.RegisterPreviousFlagsAsHidden();
cl.RegisterFloatOption("pctSim", &minPctSimilarity, "Minimum percent similarity to trigger a match to an adapter.",
CommandLineParser::PositiveFloat);
cl.RegisterIntOption("indel", &indel, "Penalty for indel (positive)", CommandLineParser::NonNegativeInteger);
cl.RegisterIntOption("minLength", &minLength, "Minimum length pass to retain.", CommandLineParser::PositiveInteger);
vector<string> opts;
cl.ParseCommandLine(argc, argv, opts);
/*
* Open all the required files, quitting if they are unavailable.
*/
ad1Reader.Init(ad1File);
ad2Reader.Init(ad2File);
reader.Init(readsFile);
ofstream splitOut;
CrucialOpen(readsOutFile, splitOut);
FASTASequence ad1, ad2;
ad1Reader.GetNext(ad1);
ad2Reader.GetNext(ad2);
FASTASequence read;
vector<int> scoreMat;
vector<Arrow> pathMat;
int readIndex = 0;
while(reader.GetNext(read)) {
read.ToUpper();
//
// Do a fitting sequence alignment to match one of the two
// adapters into the read.
//
vector<int> passStarts, passLengths, la;
read.PrintSeq(cout);
SplitRead(read, 0, read.length, ad1, ad2,
indel,
passStarts, passLengths,la, 0,
scoreMat, pathMat, minPctSimilarity, minLength);
int i;
for (i = 0; i < passStarts.size(); i++) {
cout << "read: " << readIndex << " pass: "******" " << passStarts[i] << " " << passLengths[i] << " " << la[i] << endl;
}
++readIndex;
}
}
int main(int argc, char* argv[]) {
CommandLineParser clp;
string refGenomeName;
string mutGenomeName;
string gffFileName;
float insRate = 0;
float delRate = 0;
float mutRate = 0;
bool lower = false;
gffFileName = "";
clp.RegisterStringOption("refGenome", &refGenomeName, "Reference genome.", true);
clp.RegisterStringOption("mutGenome", &mutGenomeName, "Mutated genome.", true);
clp.RegisterPreviousFlagsAsHidden();
clp.RegisterStringOption("gff", &gffFileName, "GFF file describing the modifications made to the genome.");
clp.RegisterFloatOption("i", &insRate, "Insertion rate: (0-1].",
CommandLineParser::NonNegativeFloat, false);
clp.RegisterFloatOption("d", &delRate, "Deletion rate: (0-1]",
CommandLineParser::NonNegativeFloat, false);
clp.RegisterFloatOption("m", &mutRate, "Mutation rate, even across all nucleotides: (0-1]",
CommandLineParser::NonNegativeFloat, false);
clp.RegisterFlagOption("lower", &lower, "Make mutations in lower case", false);
vector<string> leftovers;
clp.ParseCommandLine(argc, argv, leftovers);
FASTAReader reader;
FASTASequence refGenome;
reader.Init(refGenomeName);
ofstream mutGenomeOut;
CrucialOpen(mutGenomeName, mutGenomeOut, std::ios::out);
ofstream gffOut;
if (gffFileName != "") {
CrucialOpen(gffFileName, gffOut, std::ios::out);
}
vector<int> insIndices, delIndices, subIndices;
int readIndex = 0;
InitializeRandomGeneratorWithTime();
while (reader.GetNext(refGenome)) {
insIndices.resize(refGenome.length);
delIndices.resize(refGenome.length);
subIndices.resize(refGenome.length);
std::fill(insIndices.begin(), insIndices.end(), false);
std::fill(delIndices.begin(), delIndices.end(), false);
std::fill(subIndices.begin(), subIndices.end(), 0);
enum ChangeType { Ins, Del, Mut, None};
float changeProb[4];
changeProb[Ins] = insRate;
changeProb[Del] = changeProb[Ins] + delRate;
changeProb[Mut] = changeProb[Del] + mutRate;
changeProb[None] = 1;
if (changeProb[Mut] > 1) {
cout << "ERROR! The sum of the error probabilities must be less than 1" << endl;
exit(1);
}
DNALength pos;
float randomNumber;
int numIns = 0;
int numDel = 0;
int numMut = 0;
for (pos =0 ; pos < refGenome.length; pos++) {
randomNumber = Random();
if (randomNumber < changeProb[Ins]) {
insIndices[pos] = true;
numIns++;
}
else if (randomNumber < changeProb[Del]) {
delIndices[pos] = true;
numDel++;
}
else if (randomNumber < changeProb[Mut]){
Nucleotide newNuc = TwoBitToAscii[RandomInt(4)];
int maxIts = 100000;
int it = 0;
while (newNuc == refGenome.seq[pos]) {
newNuc = TwoBitToAscii[RandomInt(4)];
if (it == maxIts) {
cout << "ERROR, something is wrong with the random number generation, it took too many tries to generate a new nucleotide" << endl;
exit(1);
}
}
subIndices[pos] = refGenome[pos];
refGenome.seq[pos] = ToLower(newNuc,lower);
++numMut;
}
}
// cout << readIndex << " m " << numMut << " i " << numIns << " d " << numDel << endl;
if (readIndex % 100000 == 0 && readIndex > 0) {
cout << readIndex << endl;
}
//
// Now add the insertions and deletions.
//
FASTASequence newSequence;
DNALength newPos;
if (numIns - numDel + refGenome.length < 0) {
cout << "ERROR, the genome has been deleted to nothing." << endl;
exit(1);
}
ResizeSequence(newSequence, refGenome.length + (numIns - numDel));
newPos = 0;
pos = 0;
for (pos = 0; pos < refGenome.length; pos++) {
assert(newPos < newSequence.length or delIndices[pos] == true);
if (subIndices[pos] != 0 and gffFileName != "") {
gffOut << refGenome.GetName() << " . SNV " << newPos << " " << newPos <<" 0.00 . . reference=" << (char)subIndices[pos] << ";confidence=10;Name=" << newPos << (char)subIndices[pos] << ">" << refGenome.seq[pos] <<";coverage=10;variantseq=" << refGenome.seq[pos] << endl;
}
if (insIndices[pos] == true) {
newSequence.seq[newPos] = ToLower(TwoBitToAscii[RandomInt(4)], lower);
newPos++;
newSequence.seq[newPos] = refGenome.seq[pos];
assert(newSequence.seq[newPos] != '1');
assert(newSequence.seq[newPos] != 1);
if (gffFileName != "") {
gffOut << refGenome.GetName() << " . deletion " << newPos << " " << newPos << " 0.00 . . reference=" << newSequence.seq[newPos] << ";length=1;confidence=10;coverage=0;Name="<< newPos << "del" << newSequence.seq[newPos] << endl;
}
newPos++;
}
else if (delIndices[pos] == true) {
// no-op, skip
if (gffFileName != "") {
gffOut << refGenome.GetName() << " . insertion " << newPos << " " << newPos << " 0.00 . . confidence=10;Name=" << newPos << "_ins" << refGenome.seq[pos] << ";reference=.;length=1;coverage=0;variantseq=" << refGenome.seq[newPos] << endl;
//ref000001 . deletion 20223 20223 0.00 . . reference=T;length=1;confidence=0;coverage=0;Name=20222delT
}
}
else {
newSequence.seq[newPos] = refGenome.seq[pos];
newPos++;
}
}
stringstream titlestrm;
titlestrm << " mutated ins " << insRate << " del " << delRate << " mut " << mutRate;
newSequence.CopyTitle(refGenome.title);
newSequence.AppendToTitle(titlestrm.str());
newSequence.PrintSeq(mutGenomeOut);
newSequence.Free();
readIndex++;
}
}
int main(int argc, char* argv[]) {
FASTAReader reader;
if (argc < 5) {
cout << "usage: wordCounter seqFile tupleSize tupleOutputFile posOutputFile" << endl;
exit(1);
}
string fileName = argv[1];
int tupleSize = atoi(argv[2]);
string tupleListName = argv[3];
string posOutName = argv[4];
TupleMetrics tm;
tm.Initialize(tupleSize);
reader.Init(fileName);
FASTASequence seq;
reader.GetNext(seq);
vector<CountedDNATuple> tupleList;
CountedDNATuple tuple;
DNALength i;
for (i = 0; i < seq.length - tm.tupleSize + 1; i++ ) {
if (tuple.FromStringRL((Nucleotide*) (seq.seq + i), tm)) {
tuple.count = i;
tupleList.push_back(tuple);
}
}
std::sort(tupleList.begin(), tupleList.end());
int t;
int t2;
int numTuples = tupleList.size();
t = t2 = 0;
int numUnique = 0;
while (t < numTuples) {
t2 = t;
t2++;
while (t2 < numTuples and tupleList[t] == tupleList[t2]) {
t2++;
}
++numUnique;
t = t2;
}
ofstream countedTupleListOut;
countedTupleListOut.open(tupleListName.c_str(), ios_base::binary);
ofstream posOut;
posOut.open(posOutName.c_str(), ios_base::binary);
countedTupleListOut.write((const char*) &numUnique, sizeof(int));
countedTupleListOut.write((const char*) &tm.tupleSize, sizeof(int));
posOut.write((const char*) &numUnique, sizeof(int));
//
// Write out the tuple+counts to a file.
//
t = t2 = 0;
CountedDNATuple countedTuple;
int numMultOne = 0;
while (t < numTuples) {
t2 = t;
t2++;
while (t2 < numTuples and tupleList[t] == tupleList[t2]) {
t2++;
}
countedTuple.tuple = tupleList[t].tuple;
countedTuple.count = t2 - t;
if (countedTuple.count == 1) ++numMultOne;
countedTupleListOut.write((const char*) &countedTuple,sizeof(CountedDNATuple));
posOut.write((char*)&countedTuple.count, sizeof(int));
int tc;
for (tc = t; tc < t2; tc++) {
posOut.write((char*) &tupleList[tc].count, sizeof(int));
}
t = t2;
}
//
// Write out the positions of the tuples to a file.
//
posOut.close();
countedTupleListOut.close();
// cout << "found " << numUnique << " distinct " << DNATuple::TupleSize << "-mers." << endl;
cout << numMultOne << endl;
return 0;
}
int main(int argc, char* argv[]) {
if (argc < 2) {
PrintUsage();
exit(1);
}
int argi = 1;
string saFile = argv[argi++];
vector<string> inFiles;
int doBLT = 1;
int bltPrefixLength = 8;
int parsingOptions = 0;
SAType saBuildType = larsson;
int read4BitCompressed = 0;
int diffCoverSize = 0;
while (argi < argc) {
if (strlen(argv[argi]) > 0 and
argv[argi][0] == '-'){
parsingOptions = 1;
}
if (!parsingOptions) {
inFiles.push_back(argv[argi]);
}
else {
if (strcmp(argv[argi], "-blt") == 0) {
doBLT = 1;
if (argi < argc - 1) {
bltPrefixLength = atoi(argv[++argi]);
if (bltPrefixLength == 0) {
cout << argv[argi] << " is not a valid lookup table length." << endl;
exit(1);
}
}
else {
cout << "Please specify a lookup table length." << endl;
exit(1);
}
}
else if (strcmp(argv[argi], "-mamy") == 0) {
saBuildType = manmy;
}
else if (strcmp(argv[argi], "-larsson") == 0) {
saBuildType = larsson;
}
else if (strcmp(argv[argi], "-mcilroy") == 0) {
saBuildType = mcilroy;
}
else if (strcmp(argv[argi], "-slow") == 0) {
saBuildType = slow;
}
else if (strcmp(argv[argi], "-kark") == 0) {
saBuildType = kark;
}
else if (strcmp(argv[argi], "-mafe") == 0) {
saBuildType = mafe;
}
else if (strcmp(argv[argi], "-welter") == 0) {
saBuildType = welter;
}
else if (strcmp(argv[argi], "-welterweight") == 0) {
if (argi < argc-1) {
diffCoverSize = atoi(argv[++argi]);
}
else {
cout << "Please specify a difference cover size. Valid values are 7,32,64,111, and 2281. Larger values use less memory but may be slower." << endl;
exit(1);
}
if ( ! (diffCoverSize == 7 or
diffCoverSize == 32 or
diffCoverSize == 64 or
diffCoverSize == 111 or
diffCoverSize == 2281) ) {
cout << "The difference cover size must be one of 7,32,64,111, or 2281." << endl;
cout << "Larger numbers use less space but are more slow." << endl;
exit(1);
}
}
else if (strcmp(argv[argi], "-4bit") == 0) {
read4BitCompressed = 1;
}
else {
PrintUsage();
cout << "ERROR, bad option: " << argv[argi] << endl;
exit(1);
}
}
++argi;
}
if (inFiles.size() == 0) {
//
// Special use case: the input file is a fasta file. Write to that file + .sa
//
inFiles.push_back(saFile);
saFile = saFile + ".sa";
}
VectorIndex inFileIndex;
FASTASequence seq;
CompressedSequence<FASTASequence> compSeq;
if (read4BitCompressed == 0) {
for (inFileIndex = 0; inFileIndex < inFiles.size(); ++inFileIndex) {
FASTAReader reader;
reader.Init(inFiles[inFileIndex]);
reader.SetSpacePadding(111);
if (saBuildType == kark) {
//
// The Karkkainen sa building method requires a little extra
// space at the end of the dna sequence so that counting may
// be done mod 3 without adding extra logic for boundaries.
//
}
if (inFileIndex == 0) {
reader.ReadAllSequencesIntoOne(seq);
reader.Close();
}
else {
while(reader.ConcatenateNext(seq)) {
cout << "added " << seq.title << endl;
}
}
}
seq.ToThreeBit();
//seq.ToUpper();
}
else {
assert(inFiles.size() == 1);
cout << "reading compressed sequence." << endl;
compSeq.Read(inFiles[0]);
seq.seq = compSeq.seq;
seq.length = compSeq.length;
compSeq.RemoveCompressionCounts();
cout << "done." << endl;
}
//
// For now, do not allow creation of suffix arrays on sequences > 4G.
//
if (seq.length >= UINT_MAX) {
cout << "ERROR, references greater than " << UINT_MAX << " bases are not supported." << endl;
cout << "Consider breaking the reference into multiple files, running alignment. " << endl;
cout << "against each file, and merging the result." << endl;
exit(1);
}
vector<int> alphabet;
SuffixArray<Nucleotide, vector<int> > sa;
// sa.InitTwoBitDNAAlphabet(alphabet);
// sa.InitAsciiCharDNAAlphabet(alphabet);
sa.InitThreeBitDNAAlphabet(alphabet);
if (saBuildType == manmy) {
sa.MMBuildSuffixArray(seq.seq, seq.length, alphabet);
}
else if (saBuildType == mcilroy) {
sa.index = new SAIndex[seq.length+1];
DNALength i;
for (i = 0; i < seq.length; i++) { sa.index[i] = seq.seq[i] + 1;}
sa.index[seq.length] = 0;
ssort(sa.index, NULL);
for (i = 1; i < seq.length+1; i++ ){ sa.index[i-1] = sa.index[i];};
sa.length = seq.length;
}
else if (saBuildType == larsson) {
sa.LarssonBuildSuffixArray(seq.seq, seq.length, alphabet);
}
else if (saBuildType == kark) {
sa.index = new SAIndex[seq.length];
seq.ToThreeBit();
DNALength p;
for (p = 0; p < seq.length; p++ ){ seq.seq[p]++; }
KarkkainenBuildSuffixArray<Nucleotide>(seq.seq, sa.index, seq.length, 5);
sa.length = seq.length;
}
else if (saBuildType == mafe) {
// sa.MaFeBuildSuffixArray(seq.seq, seq.length);
}
else if (saBuildType == welter) {
if (diffCoverSize == 0) {
sa.LightweightBuildSuffixArray(seq.seq, seq.length);
}
else {
sa.LightweightBuildSuffixArray(seq.seq, seq.length, diffCoverSize);
}
}
if (doBLT) {
sa.BuildLookupTable(seq.seq, seq.length, bltPrefixLength);
}
sa.Write(saFile);
return 0;
}
int main(int argc, char* argv[]) {
string inFileName, readsFileName;
DNALength readLength;
float coverage = 0;
bool noRandInit = false;
int numReads = -1;
CommandLineParser clp;
int qualityValue = 20;
bool printFastq = false;
int stratify = 0;
string titleType = "pacbio";
string fastqType = "illumina"; // or "sanger"
clp.RegisterStringOption("inFile", &inFileName, "Reference sequence", 0);
clp.RegisterPreviousFlagsAsHidden();
clp.RegisterIntOption("readLength", (int*) &readLength, "The length of reads to simulate. The length is fixed.",
CommandLineParser::PositiveInteger, "Length of every read.", 0);
clp.RegisterFloatOption("coverage", &coverage, "Total coverage (from which the number of reads is calculated",
CommandLineParser::PositiveFloat, 0);
clp.RegisterFlagOption("nonRandInit", &noRandInit, "Skip initializing the random number generator with time.");
clp.RegisterIntOption("nReads", &numReads, "Total number of reads (from which coverage is calculated)", CommandLineParser::PositiveInteger, 0);
clp.RegisterStringOption("readsFile", &readsFileName, "Reads output file", 0);
clp.RegisterFlagOption("fastq", &printFastq, "Fake fastq output with constant quality value (20)");
clp.RegisterIntOption("quality", &qualityValue, "Value to use for fastq quality", CommandLineParser::PositiveInteger);
clp.RegisterIntOption("stratify", &stratify, "Sample a read every 'stratify' bases, rather than randomly.", CommandLineParser::PositiveInteger);
clp.RegisterStringOption("titleType", &titleType, "Set the name of the title: 'pacbio'|'illumina'");
clp.RegisterStringOption("fastqType", &fastqType, "Set the type of fastq: 'illumina'|'sanger'");
vector<string> leftovers;
clp.ParseCommandLine(argc, argv, leftovers);
if (!noRandInit) {
InitializeRandomGeneratorWithTime();
}
FASTAReader inReader;
inReader.Init(inFileName);
vector<FASTASequence> reference;
inReader.ReadAllSequences(reference);
ofstream readsFile;
if (readsFileName == "") {
cout << "ERROR. You must specify a reads file." << endl;
exit(0);
}
CrucialOpen(readsFileName, readsFile, std::ios::out);
ofstream sangerFastqFile;
if (fastqType == "sanger") {
string sangerFastqFileName = readsFileName + ".fastq";
CrucialOpen(sangerFastqFileName, sangerFastqFile, std::ios::out);
}
DNALength refLength = 0;
int i;
for (i = 0; i < reference.size(); i++) {
refLength += reference[i].length;
}
if (numReads == -1 and coverage == 0 and stratify == 0) {
cout << "Error, you must specify either coverage, nReads, or stratify." << endl;
exit(1);
}
else if (numReads == -1) {
numReads = (refLength / readLength) * coverage;
}
if (stratify) {
if (!readLength) {
cout << "ERROR. If you are using stratification, a read length must be specified." << endl;
exit(1);
}
}
DNASequence sampleSeq;
sampleSeq.length = readLength;
int maxRetry = 10000000;
int retryNumber = 0;
DNALength seqIndex, seqPos;
if (stratify) {
seqIndex = 0;
seqPos = 0;
}
DNALength origReadLength = readLength;
for (i = 0; stratify or i < numReads; i++) {
if (stratify == 0) {
FindRandomPos(reference, seqIndex, seqPos, readLength );
}
else {
//
// find the next start pos, or bail if done
//
if (seqPos >= reference[seqIndex].length) {
if (seqIndex == reference.size() - 1) {
break;
}
else {
seqIndex = seqIndex + 1;
seqPos = 0;
continue;
}
}
readLength = min(reference[seqIndex].length - seqPos, origReadLength);
}
sampleSeq.seq = &reference[seqIndex].seq[seqPos];
int j;
int gappedRead = 0;
string title;
stringstream titleStrm;
if (titleType == "pacbio") {
titleStrm << i << "|"<< reference[seqIndex].GetName() << "|" << seqPos << "|" << seqPos + readLength;
}
else if (titleType == "illumina") {
titleStrm << "SE_" << i << "_0@" << seqPos << "-"<<seqPos+readLength <<"/1";
}
else {
cout << "ERROR. Bad title type " << titleType << endl;
exit(0);
}
title = titleStrm.str();
sampleSeq.length = readLength;
if (!printFastq) {
readsFile << ">" << title << endl;
sampleSeq.PrintSeq(readsFile);
}
else {
FASTQSequence fastqSampleSeq;
fastqSampleSeq.CopyTitle(title);
fastqSampleSeq.seq = sampleSeq.seq;
fastqSampleSeq.length = sampleSeq.length;
fastqSampleSeq.qual.data = new unsigned char[sampleSeq.length];
fill(fastqSampleSeq.qual.data, fastqSampleSeq.qual.data + sampleSeq.length, qualityValue);
if (fastqType == "illumina") {
fastqSampleSeq.PrintFastq(readsFile, fastqSampleSeq.length+1);
}
else {
fastqSampleSeq.PrintSeq(readsFile);
fastqSampleSeq.PrintQual(sangerFastqFile);
}
delete[] fastqSampleSeq.qual.data;
delete[] fastqSampleSeq.title;
}
if (stratify) {
seqPos += readLength;
}
}
return 0;
}
int main(int argc, char* argv[]) {
if (argc < 4) {
PrintUsage();
exit(0);
}
string rgFileName, vertexSeqFileName, scaffoldDirName;
rgFileName = argv[1];
vertexSeqFileName = argv[2];
scaffoldDirName = argv[3];
string repeatFileName = "";
bool printRepeatsSeparately = false;
int argi = 4;
bool printSeparate=false;
while (argi < argc) {
if (strcmp(argv[argi], "-separate") == 0) {
printSeparate=true;
}
else if (strcmp(argv[argi], "-repeats") == 0) {
printRepeatsSeparately = true;
repeatFileName = argv[++argi];
}
else {
cout << "bad option: " << argv[argi] << endl;
PrintUsage();
exit(1);
}
++argi;
}
FASTAReader vertexSequenceReader;
vertexSequenceReader.Init(vertexSeqFileName);
//
// Input necessary data
//
vector<FASTASequence> vertexSequences;
vertexSequenceReader.ReadAllSequences(vertexSequences);
RepeatGraph<string> rg;
rg.ReadGraph(rgFileName);
vector<FASTASequence> vertexRCSequences;
VectorIndex vertexIndex;
vertexRCSequences.resize(vertexSequences.size());
for (vertexIndex = 0; vertexIndex < vertexSequences.size(); vertexIndex++ ){
vertexSequences[vertexIndex].MakeRC(vertexRCSequences[vertexIndex]);
}
VectorIndex outEdgeIndex;
int scaffoldIndex = 0;
ofstream scaffoldOut;
if (printSeparate==false) {
// scaffold dir name is really a file name here.
CrucialOpen(scaffoldDirName, scaffoldOut, std::ios::out);
}
for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++ ){
rg.vertices[vertexIndex].traversed = false;
}
//
// Set up flow for calling multiplicity.
//
/*
Test all this out later.
AssignMinimumFlowToEdges(rg, 2);
AssignVertexFlowBalance(rg);
BalanceKirchhoffFlow(rg);
UInt edgeIndex;
for (edgeIndex = 0; edgeIndex < rg.edges.size(); edgeIndex++) {
if (rg.edges[edgeIndex].flow > 1) {
cout << edgeIndex << " " << rg.edges[edgeIndex].flow << endl;
}
}
*/
int numPrintedVertices = 0;
for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++ ){
//
// Look to see if this vertex is a branching vertex.
//
if ((rg.vertices[vertexIndex].inEdges.size() != 1 or
rg.vertices[vertexIndex].outEdges.size() != 1) and
rg.vertices[vertexIndex].traversed == false) {
//
// This is a branching vertex. Print all paths from this vertex, but not the vertex
// itself if it appears repetitive.
//
VectorIndex outEdgeIndex;
bool printedThisVertex = false;
for (outEdgeIndex = 0; outEdgeIndex < rg.vertices[vertexIndex].outEdges.size(); outEdgeIndex++ ){
//
// This is a branching vertex.
//
VectorIndex pathIndex;
stringstream scaffoldFileNameStrm;
cout << " printing scaffold: " << scaffoldIndex << endl;
if (printSeparate) {
scaffoldFileNameStrm << scaffoldDirName << "/" << scaffoldIndex << ".fasta";
string scaffoldFileName = scaffoldFileNameStrm.str();
CrucialOpen(scaffoldFileName, scaffoldOut, std::ios::out);
}
++scaffoldIndex;
//
// Store the nonbranching path in a list so that it may be quickly processed.
//
bool pathIsPrinted = false;
vector<VectorIndex> path;
if (rg.vertices[vertexIndex].InDegree() == 0 and rg.vertices[vertexIndex].OutDegree() == 1) {
path.push_back(vertexIndex);
}
VectorIndex pathVertex = rg.edges[rg.vertices[vertexIndex].outEdges[outEdgeIndex]].dest;
while(rg.vertices[pathVertex].inEdges.size() == 1 and
rg.vertices[pathVertex].outEdges.size() == 1) {
if (rg.vertices[pathVertex].traversed == true) {
pathIsPrinted = true;
break;
}
path.push_back(pathVertex);
// Mark the forward and reverse complement as traversed.
pathVertex = rg.edges[rg.vertices[pathVertex].outEdges[0]].dest;
//
}
//
// Look to see if this is the end of a simple path, if so, add it to the scaffold.
//
pathVertex = rg.edges[rg.vertices[vertexIndex].outEdges[outEdgeIndex]].dest;
if (rg.vertices[pathVertex].OutDegree() == 0 and rg.vertices[pathVertex].InDegree() == 1) {
path.push_back(pathVertex);
}
//
// Determine the sequences in the scaffold and the total scaffold length.
//
if (pathIsPrinted == false) {
VectorIndex p;
DNALength scaffoldLength = 0;
for (p = 0; p < path.size(); p++ ){
scaffoldLength += vertexSequences[path[p]/2].length;
rg.vertices[path[p]].traversed = true;
// rg.vertices[2*(path[p]/2)+ !(path[p]%2)].traversed = true;
++numPrintedVertices;
}
cout << "path is of size " << path.size() << " length " << scaffoldLength << endl;
if (!printSeparate) {
scaffoldOut << ">" << scaffoldIndex << " " << path.size() << " " << scaffoldLength << endl;
}
for (p = 0; p < path.size(); p++) {
if (printSeparate) {
scaffoldOut << ">" << p << " " << path[p]/2 << " " << vertexSequences[path[p]/2].length << endl;
}
if (path[p]%2 == 0) {
((DNASequence)vertexSequences[path[p]/2]).PrintSeq(scaffoldOut);
}
else {
((DNASequence)vertexRCSequences[path[p]/2]).PrintSeq(scaffoldOut);
}
rg.vertices[path[p]].traversed = true;
rg.vertices[2*(path[p]/2) + !(path[p]%2)].traversed = true;
}
if (printSeparate) {
scaffoldOut.close();
scaffoldOut.clear();
}
}
}
}
}
ofstream* outPtr;
ofstream repeatOut;
if (printRepeatsSeparately) {
CrucialOpen(repeatFileName, repeatOut, std::ios::out);
outPtr = &repeatOut;
}
else {
outPtr = &scaffoldOut;
}
for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++ ){
if (rg.vertices[vertexIndex].traversed == false) {
//
// Print this vertex sequence only. It is repetitive, or isolated.
//
*outPtr << ">" << scaffoldIndex << endl;
++scaffoldIndex;
if (vertexIndex%2 == 0) {
((DNASequence)vertexSequences[vertexIndex/2]).PrintSeq(*outPtr);
}
else {
((DNASequence)vertexRCSequences[vertexIndex/2]).PrintSeq(*outPtr);
}
rg.vertices[vertexIndex].traversed = true;
rg.vertices[2*(vertexIndex/2)+ !(vertexIndex%2)].traversed = true;
}
}
cout << "printed: " << numPrintedVertices << " of " << rg.vertices.size() << endl;
}
int main(int argc, char* argv[]) {
string rgInName, rgOutName;
int minPathLength;
string vertexSequenceFileName;
if (argc < 5) {
cout << "usage: trimShortEnds in.rg vertexSequences minPathLength out.rg" << endl;
exit(1);
}
rgInName = argv[1];
vertexSequenceFileName = argv[2];
minPathLength = atoi(argv[3]);
rgOutName = argv[4];
ofstream rgOut;
CrucialOpen(rgOutName, rgOut, std::ios::out);
FASTAReader vertexSequenceReader;
vertexSequenceReader.Init(vertexSequenceFileName);
RepeatGraph<string> rg;
vector<FASTASequence> vertexSequences;
rg.ReadGraph(rgInName);
vertexSequenceReader.ReadAllSequences(vertexSequences);
VectorIndex vertexIndex;
VectorIndex outEdgeIndex;
VectorIndex edgeIndex;
if (rg.edges.size() == 0) {
cout << "LIKELY INVALID GRAPH. There are no edges." << endl;
return 0;
}
//
// At first, any edge that exists is connected to a vertex. This
// will change as low coverage edges are deleted and replaced by
// high coverage edges from the end of the array.
//
for (edgeIndex = 0; edgeIndex < rg.edges.size(); edgeIndex++) {
rg.edges[edgeIndex].connected = true;
}
set<std::pair<VectorIndex, VectorIndex> > srcDestToRemove;
for (vertexIndex = 0; vertexIndex < rg.vertices.size(); vertexIndex++) {
if (rg.vertices[vertexIndex].inEdges.size() == 0 and
rg.vertices[vertexIndex].outEdges.size() == 1) {
//
// This is a source. Traverse this until a branching vertex or the end is found.
//
vector<VectorIndex> path;
path.push_back(vertexIndex);
int pathLength = 0;
VectorIndex pathVertex;
VectorIndex pathEdge;
pathEdge = rg.vertices[vertexIndex].outEdges[0];
pathVertex = rg.edges[pathEdge].dest;
while (rg.vertices[pathVertex].inEdges.size() == 1 and
rg.vertices[pathVertex].outEdges.size() == 1) {
path.push_back(pathVertex);
pathEdge = rg.vertices[pathVertex].outEdges[0];
pathVertex = rg.edges[pathEdge].dest;
pathLength += vertexSequences[pathVertex/2].length;
}
pathLength += vertexSequences[pathVertex/2].length;
path.push_back(pathVertex);
if (pathLength < minPathLength and path.size() < 3) {
//
// Remove this path, it is too short.
// Also remove the complement.
//
cout << "trimming path of " << path.size() << " is of sequence length " << pathLength << endl;
VectorIndex pathIndex;
for (pathIndex = 0; pathIndex < path.size() - 1; pathIndex++) {
srcDestToRemove.insert(pair<VectorIndex, VectorIndex>(path[pathIndex], path[pathIndex+1]));
srcDestToRemove.insert(pair<VectorIndex, VectorIndex>(2*(path[pathIndex+1]/2) + !(path[pathIndex+1]%2),
2*(path[pathIndex]/2) + !(path[pathIndex]%2)));
}
}
}
}
MarkEdgePairsForRemoval(srcDestToRemove, rg.vertices, rg.edges);
RemoveUnconnectedEdges(rg.vertices, rg.edges);
rg.WriteGraph(rgOut);
return 0;
}
int main(int argc, char* argv[]) {
string genomeFileName;
string suffixArrayFileName;
if (argc < 4) {
cout << "Usage: printWordCount genome suffixArray k [k2 k3 k4...]" << endl;
exit(1);
}
genomeFileName = argv[1];
suffixArrayFileName = argv[2];
int argi = 3;
vector<DNALength> k;
while (argi < argc) {
k.push_back(atoi(argv[argi]));
argi++;
}
// Get the ref sequence.
FASTAReader reader;
reader.Init(genomeFileName);
FASTASequence seq;
// reader.GetNext(seq);
reader.ReadAllSequencesIntoOne(seq);
seq.ToUpper();
// Get the suffix array.
DNASuffixArray sarray;
sarray.Read(suffixArrayFileName);
int ki;
char *word;
cout << "wordlen word nword" << endl;
for (ki = 0; ki < k.size(); ki++) {
word = new char[k[ki]+1];
word[k[ki]] = '\0';
DNALength i;
DNALength numUnique = 0;
for (i = 0; i < seq.length - k[ki] - 1; ) {
DNALength j = i + 1;
bool seqAtN = false;
int si;
for(si = 0; si < k[ki]; si++) {
if (seq.seq[sarray.index[i] + si] == 'N') {
seqAtN = true;
break;
}
}
if (seqAtN) {
i++;
continue;
}
while (j < seq.length - k[ki] and
seq.length - sarray.index[i] >= k[ki] and
seq.length - sarray.index[j] >= k[ki] and
strncmp((const char*) &seq.seq[sarray.index[i]], (const char*) &seq.seq[sarray.index[j]], k[ki]) == 0) {
j++;
}
if (seq.length - sarray.index[i] >= k[ki]) {
for(si = 0; si < k[ki]; si++) {
word[si] = seq.seq[sarray.index[i]+si];
}
cout << k[ki] << " " << word << " " << j - i + 1 << endl;
if (j == i + 1) {
++numUnique;
}
}
i = j;
}
}
}
int main(int argc, char* argv[]) {
FASTAReader reader;
FASTASequence read;
int maxLength = 100;
if (argc < 3) {
cout << "usage: pairAlignAllContigs inFile maxLength equivalencies [-minIdent i]" << endl;
exit(0);
}
string readsFileName, equivalenciesFileName;
readsFileName = argv[1];
maxLength = atoi(argv[2]);
equivalenciesFileName = argv[3];
int argi = 4;
float minIdentity = 80;
while (argi < argc) {
if (strcmp(argv[argi], "-minIdent") == 0) {
minIdentity = atoi(argv[++argi]);
}
++argi;
}
vector<FASTASequence> reads, readsRC;;
reader.Init(readsFileName);
reader.ReadAllSequences(reads);
readsRC.resize(reads.size());
int r;
for (r =0; r < reads.size();r++) {
reads[r].MakeRC(readsRC[r]);
}
ofstream equivOut;
CrucialOpen(equivalenciesFileName, equivOut);
Matrix<int> alignScores;
Matrix<float> alignIdentities;
alignScores.Resize(reads.size(), reads.size());
alignIdentities.Resize(reads.size(), reads.size());
vector<int> scoreMat;
vector<Arrow> pathMat;
int i, j;
int alignScore;
FASTASequence readi, readj;
FASTASequence rcReadi, rcReadj;
for (i = 0; i < reads.size(); i++) {
float maxFrontIdent, maxEndIdent;
int maxFrontIdentIndex, maxEndIdentIndex;
maxFrontIdent = 0; maxEndIdent = 0;
maxFrontIdentIndex = 0;
maxEndIdentIndex = 0;
int maxFrontIdentLength = 0;
int maxEndIdentLength = 0;
int maxFrontLength = 0;
int maxEndLength = 0;
int nmaxFrontLengthIndex = 0;
int maxEndLengthIndex = 0;
float maxFrontLengthIdent = 0;
float maxEndLengthIdent = 0;
int maxFrontLengthIndex = 0;
equivOut << reads[i].GetName();
for (j = 0; j < reads.size(); j++ ){
//
// Store the two ends of the alignment.
//
alignScore = 0;
int rcAlignScore;
Alignment alignment;
Alignment rcAlignment;
Alignment *optAlignment;
if (i != j) {
if (reads[i].length < maxLength and reads[j].length < maxLength) {
alignScore = SWAlign(reads[i], reads[j], SMRTDistanceMatrix, 3, scoreMat, pathMat, alignment, Global);
}
if (reads[i].length < maxLength and reads[j].length < maxLength) {
rcAlignScore = SWAlign(reads[i], readsRC[j], SMRTDistanceMatrix, 3, scoreMat, pathMat, rcAlignment, Global);
}
ComputeAlignmentStats(alignment, reads[i].seq, reads[j].seq, SMRTDistanceMatrix, 3,3 );
ComputeAlignmentStats(rcAlignment, reads[i].seq, readsRC[j].seq, SMRTDistanceMatrix, 3,3 );
if (alignment.pctSimilarity > minIdentity or rcAlignment.pctSimilarity > minIdentity) {
equivOut << " " << reads[j].GetName();
}
}
}
equivOut << endl;
}
return 0;
}
