public BgBrick(String sFile) {
try {
richSeq =
RichSequence.IOTools.readGenbankDNA(new BufferedReader(new FileReader(sFile)), null)
.nextRichSequence();
} catch (Exception e) {
e.printStackTrace();
}
locus = richSeq.getName();
seqLen = richSeq.length();
sSeq = richSeq.seqString();
}
@Option(
help = "Input sequences (output the intersecting sequences rather than a new GFF file)",
optional = true)
public void setSeqs(File f)
throws FileNotFoundException, ChangeVetoException, NoSuchElementException, BioException {
this.seqsFile = f;
this.seqDB = new HashSequenceDB();
for (SequenceIterator si =
RichSequence.IOTools.readFastaDNA(new BufferedReader(new FileReader(f)), null);
si.hasNext(); ) {
seqDB.addSequence(si.nextSequence());
}
}
public void main(String[] args) throws BioException, IOException {
if (count.length != args.length) {
System.err.println("The number of counts and output file arguments does not match!");
System.exit(1);
}
OutputStream[] outputStreams;
if ((args != null) && (args.length > 0)) {
outputStreams = new OutputStream[args.length];
for (int i = 0; i < args.length; i++) {
outputStreams[i] = new BufferedOutputStream(new FileOutputStream(args[i]));
}
} else {
outputStreams = new OutputStream[] {System.out};
}
RichSequenceIterator seqIterator =
RichSequence.IOTools.readFastaDNA(new BufferedReader(new FileReader(seqFile)), null);
List<Sequence> seqs = new ArrayList<Sequence>();
while (seqIterator.hasNext()) {
seqs.add(seqIterator.nextSequence());
}
List<List<Sequence>> chosenSeqs = new ArrayList<List<Sequence>>();
if (!sampleWithReplacement) {
for (int c : count) {
List<Sequence> cseqs = new ArrayList<Sequence>();
chosenSeqs.add(cseqs);
while (c > 0) {
int randSeqIndex = random.nextInt(seqs.size());
cseqs.add(seqs.remove(randSeqIndex));
c--;
}
}
} else if (sampleWithReplacement || (length > 0)) {
/*
* if you want to sample from sequences with replacement
* or if the wanted length is specified
*/
for (int c : count) {
int i = 0;
List<Sequence> cseqs = new ArrayList<Sequence>();
chosenSeqs.add(cseqs);
while (c > 0) {
Sequence randomSeq = seqs.get(random.nextInt(seqs.size()));
if (length > 0) {
int startPos = random.nextInt(1 + randomSeq.length() - length);
cseqs.add(
new SimpleSequence(
randomSeq.subList(startPos, startPos + length),
null,
randomSeq.getName() + "_" + i++,
Annotation.EMPTY_ANNOTATION));
} else {
cseqs.add(randomSeq);
}
c--;
}
}
}
int i = 0;
for (List<Sequence> seqList : chosenSeqs) {
for (Sequence seq : seqList) {
Sequence s;
if (uniqueNames) {
s =
new SimpleSequence(
seq.subList(1, seq.length()),
null,
seq.getName() + "_" + i,
Annotation.EMPTY_ANNOTATION);
} else {
s = seq;
}
RichSequence.IOTools.writeFasta(outputStreams[i], s, null);
outputStreams[i].flush();
}
i++;
}
seqs = null;
}
/**
* @param args
* @throws Exception
*/
public void main(String[] args) throws Exception {
List<Map<String, Location>> locs = new ArrayList<Map<String, Location>>();
for (String fileName : args) {
locs.add(GFFUtils.gffToLocationMap(new File(fileName)));
}
Set<String> seqIds;
{
Iterator<Map<String, Location>> i = locs.iterator();
seqIds = new HashSet<String>(i.next().keySet());
while (i.hasNext()) {
seqIds.retainAll(i.next().keySet());
}
}
if (validate && (seqDB != null)) {
for (Map<String, Location> ls : locs) {
WriteCoveredSequences.validateGFFSequenceIdentifiersAgainstSequences(ls, seqDB);
}
}
PrintWriter pw = null;
GFFWriter gffw = null;
GFFEntrySet gffEntries = null;
if (outputFormat == Format.GFF) {
pw = new PrintWriter(new OutputStreamWriter(System.out));
gffw = new GFFWriter(pw);
} else {
gffEntries = new GFFEntrySet();
}
for (String id : seqIds) {
Iterator<Map<String, Location>> i = locs.iterator();
Location l = i.next().get(id);
while (i.hasNext()) {
l = LocationTools.intersection(l, i.next().get(id));
}
if (negate) {
l = LocationTools.subtract(new RangeLocation(1, seqDB.getSequence(id).length()), l);
}
SimpleGFFRecord r = new SimpleGFFRecord();
r.setSeqName(id);
r.setFeature("block");
r.setSource("nmintersectseq");
r.setStrand(StrandedFeature.POSITIVE);
for (Iterator<?> bi = l.blockIterator(); bi.hasNext(); ) {
Location bloc = (Location) bi.next();
r.setStart(bloc.getMin());
r.setEnd(bloc.getMax());
r.setComment("");
r.setGroupAttributes(new HashMap<Object, Object>());
if (gffw != null) {
gffw.recordLine(r);
} else {
Sequence seq =
new SimpleSequence(
seqDB.getSequence(id).subList(bloc.getMin(), bloc.getMax()),
null,
String.format("%s_|%d-%d|", id, bloc.getMin(), bloc.getMax()),
Annotation.EMPTY_ANNOTATION);
RichSequence.IOTools.writeFasta(System.out, seq, null);
}
}
}
if (pw != null) pw.flush();
if (seqDB != null) {
System.err.println("Writing output sequences...");
GFFTools.annotateSequences(seqDB, gffEntries);
}
}