public void parseInputFile(File inputFile) throws IOException {
geneFeatures.clear();
otherRecords.clear();
try {
GFFEntrySet gffEntries = GFFTools.readGFF(inputFile);
Iterator itr = gffEntries.lineIterator();
int count = 0;
int intronFeatures = 0;
LinkedList<GFFRecord> cdsRecs = new LinkedList<GFFRecord>();
while (itr.hasNext()) {
Object val = itr.next();
if (val instanceof GFFRecord) {
GFFRecord rec = (GFFRecord) val;
count += 1;
if (rec.getFeature().endsWith("gene")) {
GeneFeatures gf = new GeneFeatures(rec);
geneFeatures.put(gf.id, gf);
} else if (rec.getFeature().equals("CDS")) {
cdsRecs.addLast(rec);
} else {
otherRecords.add(rec);
}
}
}
for (GFFRecord rec : cdsRecs) {
Map<String, List<String>> attrs = decodeAttrMap(rec);
if (geneFeatures.containsKey(attrs.get("Parent").get(0))) {
geneFeatures.get(attrs.get("Parent").get(0)).addCDS(rec, attrs);
} else {
System.err.println("Unknown CDS Parent: " + attrs.get("Parent").get(0));
}
}
for (String k : geneFeatures.keySet()) {
GeneFeatures gf = geneFeatures.get(k);
if (gf.cds != null && gf.cds.size() > 1) {
intronFeatures++;
}
}
System.err.println("# GFF Records: " + count);
System.err.println("# Gene Feature Sets: " + geneFeatures.size());
System.err.println("\t# Intron-Features: " + intronFeatures);
} catch (ParserException e) {
e.printStackTrace();
} catch (BioException e) {
e.printStackTrace();
}
}
/**
* @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);
}
}