public static String getChrom(String chromName) {
Matcher m = chromPattern.matcher(chromName);
if (!m.matches()) {
return chromName;
}
return m.group(1);
}
public static String removePrimerLR(String pname) {
Matcher m = primerLRPattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
return m.group(1);
}
public static int[] decodePrimerName(String pname) {
Matcher m = primerNamePattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
int[] a = new int[3];
a[0] = Integer.parseInt(m.group(1));
a[1] = Integer.parseInt(m.group(2));
a[2] = Integer.parseInt(m.group(3));
return a;
}
public class ProbesFromPrimers {
public static void main(String[] args) {
try {
Genome g = Organism.findGenome(args[0]);
File blasttab = new File(args[1]);
ProbesFromPrimers pfp = new ProbesFromPrimers(g, blasttab);
Collection<NamedRegion> probes = pfp.parseProbes();
for (NamedRegion probe : probes) {
String probeName = probe.getName();
System.out.println(
String.format(
"%s\t%s\t%d\t%d", probeName, probe.getChrom(), probe.getStart(), probe.getEnd()));
}
} catch (NotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
private File blasttab;
private Genome genome;
public ProbesFromPrimers(Genome g, File bt) {
genome = g;
blasttab = bt;
}
public Collection<NamedRegion> parseProbes() throws IOException {
double ethreshold = 1.0e-3;
Parser<BlastTabEntry> parser =
new Parser<BlastTabEntry>(blasttab, new BlastTabEntry.ParsingMapper());
Iterator<BlastTabEntry> itr =
new FilterIterator<BlastTabEntry, BlastTabEntry>(
new BlastTabEntry.ExpectedScoreFilter(ethreshold), parser);
Map<String, Set<Region>> primerHits = new TreeMap<String, Set<Region>>();
Set<String> primerNames = new TreeSet<String>();
while (itr.hasNext()) {
BlastTabEntry entry = itr.next();
NamedRegion r = createNamedRegion(entry);
if (!primerHits.containsKey(entry.getQuery())) {
primerHits.put(entry.getQuery(), new HashSet<Region>());
}
primerHits.get(entry.getQuery()).add(r);
primerNames.add(removePrimerLR(entry.getQuery()));
}
LinkedList<NamedRegion> probes = new LinkedList<NamedRegion>();
for (String primerName : primerNames) {
Pair<Region, Region> hits = findProbePair(primerName, primerHits);
if (hits != null) {
Region left = hits.getFirst(), right = hits.getLast();
int start = Math.min(left.getStart(), right.getStart());
int end = Math.max(left.getEnd(), right.getEnd());
NamedRegion probe = new NamedRegion(genome, left.getChrom(), start, end, primerName);
probes.addLast(probe);
}
}
return probes;
}
public NamedRegion createNamedRegion(BlastTabEntry e) {
int start = Math.min(e.getSubjectStart(), e.getSubjectEnd());
int end = Math.max(e.getSubjectStart(), e.getSubjectEnd());
String chrom = getChrom(e.getSubject());
return new NamedRegion(genome, chrom, start, end, e.getQuery());
}
private Pair<Region, Region> findProbePair(
String primerName, Map<String, Set<Region>> primerHits) {
String leftName = String.format("%s_left", primerName);
String rightName = String.format("%s_right", primerName);
if (!primerHits.containsKey(leftName) || !primerHits.containsKey(rightName)) {
return null;
}
if (primerHits.get(leftName).size() != 1 || primerHits.get(rightName).size() != 1) {
return null;
}
Iterator<Region> leftitr = primerHits.get(leftName).iterator();
Iterator<Region> rightitr = primerHits.get(rightName).iterator();
Region left = leftitr.next();
Region right = rightitr.next();
if (!left.getChrom().equals(right.getChrom())) {
return null;
}
return new Pair<Region, Region>(left, right);
}
public static Pattern primerLRPattern =
Pattern.compile("(\\d+_\\d+_\\d+)_(?:(?:left)|(?:right))");
public static Pattern primerNamePattern =
Pattern.compile("([\\d]+)_([\\d]+)_([\\d]+)_(?:(?:left)|(?:right))");
public static Pattern chromPattern = Pattern.compile("(?:chr)?(.*)");
public static String removePrimerLR(String pname) {
Matcher m = primerLRPattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
return m.group(1);
}
public static int[] decodePrimerName(String pname) {
Matcher m = primerNamePattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
int[] a = new int[3];
a[0] = Integer.parseInt(m.group(1));
a[1] = Integer.parseInt(m.group(2));
a[2] = Integer.parseInt(m.group(3));
return a;
}
public static String getChrom(String chromName) {
Matcher m = chromPattern.matcher(chromName);
if (!m.matches()) {
return chromName;
}
return m.group(1);
}
}