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[1]) {
if (argc < 3) {
cout << "Usage: findUnique genome.fasta query.fasta effective_k [options]" << endl;
cout << " genome.fasta.sa must exist." << endl;
cout << " Finds sequences at least effective_k in length that are unique." << endl;
cout << " -max m Allow up to m matches" << endl;
cout << " -minLength l Ensure the length of the match is at least this." << endl;
cout << " -prefix p n Allow up to n matches across a prefix of length p" << endl;
cout << " -suffix s n Allow up to n matches across a suffix of length s" << endl;
cout << " Prefix and suffix options override max." << endl;
cout << " -out file Print queries to this output file (query.fasta.queries)" << endl;
exit(0);
}
DNASuffixArray sarray;
string genomeFileName = argv[1];
string suffixArrayFileName = genomeFileName + ".sa";
FASTAReader reader;
FASTASequence genome;
int maxN = 0;
int prefix = 0;
int suffix = 0;
int prefixN = 0;
int suffixN = 0;
int argi = 4;
string outputFileName = "";
int minLength = 0;
while (argi < argc) {
if (strcmp(argv[argi], "-max") == 0) {
++argi;
maxN = atoi(argv[argi]);
}
else if (strcmp(argv[argi], "-prefix") == 0) {
++argi;
prefix = atoi(argv[argi]);
++argi;
prefixN = atoi(argv[argi]);
}
else if (strcmp(argv[argi], "-suffix") == 0) {
++argi;
suffix = atoi(argv[argi]);
++argi;
suffixN = atoi(argv[argi]);
}
else if (strcmp(argv[argi], "-out") == 0) {
++argi;
outputFileName = argv[argi];
}
else if (strcmp(argv[argi], "-minLength") == 0) {
++argi;
minLength = atoi(argv[argi]);
}
++argi;
}
reader.Initialize(genomeFileName);
reader.ReadAllSequencesIntoOne(genome);
sarray.Read(suffixArrayFileName);
FASTAReader queryReader;
FASTASequence querySequence;
string queryFileName = argv[2];
int maxLength = atoi(argv[3]);
string summaryTableFileName = queryFileName + ".summary";
if (outputFileName == "") {
outputFileName = queryFileName + ".queries";
}
ofstream summaryTable(summaryTableFileName.c_str());
ofstream outputFile(outputFileName.c_str());
queryReader.Initialize(queryFileName);
while (queryReader.GetNext(querySequence)) {
int i;
cerr << "searching " << querySequence.title << endl;
if (querySequence.length < maxLength) {
continue;
}
int nMatches = 0;
querySequence.ToUpper();
int localMax;
for (i = 0; i < querySequence.length - maxLength + 1; i++) {
if ((i + 1) % 100000 == 0) {
cerr << "processed: " << i + 1 << endl;
}
int lcpLength;
vector<SAIndex> lcpLeftBounds, lcpRightBounds;
vector<SAIndex> rclcpLeftBounds, rclcpRightBounds;
localMax = maxN;
if (i < prefix) {
localMax = prefixN;
}
if (i >= querySequence.length - suffix) {
localMax = suffixN;
}
if (querySequence.length - i <= maxLength) {
continue;
}
if (querySequence.seq[i] == 'N') {
continue;
}
lcpLength = sarray.StoreLCPBounds(genome.seq, genome.length, // The string which the suffix array is built on.
&querySequence.seq[i], querySequence.length-i,
true,
maxLength,
lcpLeftBounds, lcpRightBounds,
false);
if (lcpLength < minLength) {
continue;
}
if (lcpLength < maxLength or
lcpRightBounds.size() == 0 or
(lcpRightBounds.size() > 0 and
lcpLeftBounds.size() > 0 and
lcpRightBounds[lcpRightBounds.size() - 1] - lcpLeftBounds[lcpLeftBounds.size()-1] <= localMax)) {
FASTASequence rc;
DNASequence subseq;
subseq.ReferenceSubstring(querySequence, i, maxLength);
subseq.MakeRC(rc);
int rclcpLength;
int numForwardMatches;
if (lcpLength == 0) {
numForwardMatches = 0;
}
else {
numForwardMatches = lcpRightBounds[lcpRightBounds.size() - 1] - lcpLeftBounds[lcpLeftBounds.size()-1];
}
rclcpLength = sarray.StoreLCPBounds(genome.seq, genome.length, // The string which the suffix array is built on.
rc.seq, maxLength,
true,
rclcpLength,
rclcpLeftBounds, rclcpRightBounds,
false);
string rcstr((const char*)rc.seq, rc.length);
if (rclcpLength < maxLength or
rclcpRightBounds.size() == 0 or
(numForwardMatches +
rclcpRightBounds[rclcpRightBounds.size() - 1] -
rclcpLeftBounds[rclcpLeftBounds.size()-1] <= localMax))
{
char* substr = new char[maxLength+1];
substr[maxLength] = '\0';
memcpy(substr, &querySequence.seq[i], maxLength);
// string substr = string((const char*) querySequence.seq, i, maxLength);
outputFile << querySequence.title << "\t" << substr << "\t" << i << endl;
++nMatches;
delete[] substr;
// }
}
rc.Free();
}
}
summaryTable << querySequence.title << "\t" << nMatches << endl;
querySequence.Free();
}
outputFile.close();
genome.Free();
}
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;
}
}
}
