Example #1
0
  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();
    }
  }
Example #2
0
 public static Map<String, List<String>> decodeAttrMap(GFFRecord rec) {
   Map<String, List<String>> map = new HashMap<String, List<String>>();
   for (Object ko : rec.getGroupAttributes().keySet()) {
     String str = (String) ko;
     Pair<String, List<String>> vals = decodeKeyValues(str);
     if (vals != null) {
       map.put(vals.getFirst(), vals.getLast());
     }
   }
   return map;
 }
Example #3
0
 public GeneFeatures(GFFRecord g) {
   if (!g.getFeature().endsWith("gene")) {
     throw new IllegalArgumentException();
   }
   gene = g;
   geneAttrs = decodeAttrMap(g);
   cds = new LinkedList<GFFRecord>();
   if (!geneAttrs.containsKey("ID")) {
     throw new IllegalArgumentException();
   }
   id = geneAttrs.get("ID").get(0);
 }
Example #4
0
    public void addCDS(GFFRecord rec, Map<String, List<String>> attrs) {
      if (!rec.getFeature().equals("CDS")) {
        throw new IllegalArgumentException();
      }
      if (attrs == null) {
        attrs = decodeAttrMap(rec);
      }
      if (!attrs.containsKey("Parent")) {
        throw new IllegalArgumentException();
      }
      if (!attrs.get("Parent").contains(id)) {
        throw new IllegalArgumentException();
      }

      cds.addLast(rec);
    }
Example #5
0
  public static void main(String[] args) {
    File inputFile =
        args.length > 0
            ? new File(args[0])
            : new File("C:\\Documents and Settings\\tdanford\\Desktop\\sacCer1.gff");

    try {
      SGDGFFParser parser = new SGDGFFParser();
      BinCalculator bincalc = new BinCalculator();
      parser.parseInputFile(inputFile);

      for (String k : parser.geneFeatures.keySet()) {
        try {
          GeneFeatures gf = parser.geneFeatures.get(k);
          StringBuffer line = new StringBuffer();
          ArrayList<Integer> starts = new ArrayList<Integer>();
          ArrayList<Integer> ends = new ArrayList<Integer>();
          for (GFFRecord cds : gf.cds) {
            starts.add(cds.getStart());
            ends.add(cds.getEnd());
          }
          if (starts.size() == 0) {
            starts.add(gf.gene.getStart());
            ends.add(gf.gene.getEnd());
          }

          Collections.sort(starts);
          Collections.sort(ends);
          String strand = "";
          if (gf.gene.getStrand() == StrandedFeature.NEGATIVE) {
            strand = "-";
          } else if (gf.gene.getStrand() == StrandedFeature.POSITIVE) {
            strand = "+";
          }
          /* dumb that we have to put this back on, but that's the UCSC standard format */
          String chrom = "chr" + Genome.fixYeastChrom(gf.gene.getSeqName());

          line.append(gf.id + "\t");
          line.append(chrom + "\t"); // do we need to get rid of roman numerals here ?
          line.append(strand + "\t");
          line.append(gf.gene.getStart() + "\t");
          line.append(gf.gene.getEnd() + "\t");
          line.append(starts.get(0) + "\t");
          line.append(ends.get(ends.size() - 1) + "\t");
          line.append(starts.size() + "\t");
          for (int i = 0; i < starts.size(); i++) {
            if (i == 0) {
              line.append(starts.get(i));
            } else {
              line.append("," + starts.get(i));
            }
          }
          line.append("\t");
          for (int i = 0; i < ends.size(); i++) {
            if (i == 0) {
              line.append(ends.get(i));
            } else {
              line.append("," + ends.get(i));
            }
          }
          line.append("\t");

          // no protein ID
          System.out.println(line);
        } catch (Exception e) {
          System.err.println(e.toString());
          e.printStackTrace();
        }
      }
      for (GFFRecord record : parser.otherRecords) {
        if (record.getFeature().equals("intron")) {
          continue;
        }

        try {
          StringBuffer line = new StringBuffer();
          line.append(bincalc.getBinFromRange(record.getStart(), record.getEnd()) + "\t");
          String strand = "";
          if (record.getStrand() == StrandedFeature.NEGATIVE) {
            strand = "-";
          } else if (record.getStrand() == StrandedFeature.POSITIVE) {
            strand = "+";
          }
          /* dumb that we have to put this back on, but that's the UCSC standard format */
          String chrom = "chr" + Genome.fixYeastChrom(record.getSeqName());
          Map<String, List<String>> attrs = decodeAttrMap(record);
          String name = "";
          if (attrs != null && attrs.containsKey("Name") && attrs.get("Name").size() > 0) {
            name = attrs.get("Name").get(0);
          } else if (attrs != null && attrs.containsKey("ID") && attrs.get("ID").size() > 0) {
            name = attrs.get("ID").get(0);
          }

          line.append(chrom + "\t");
          line.append(record.getStart() + "\t" + record.getEnd() + "\t");
          line.append(name + "\t");
          line.append(record.getScore() + "\t");
          line.append(strand + "\t");
          line.append(record.getFeature());
          System.out.println(line);
        } catch (Exception e) {
          System.err.println(e.toString());
          e.printStackTrace();
        }
      }

    } catch (IOException e) {
      e.printStackTrace();
    }
  }