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add upstream/downstream ref
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@heuermh
heuermh committed Aug 16, 2024
1 parent 9f30c15 commit f4a3099
Showing 1 changed file with 68 additions and 15 deletions.
83 changes: 68 additions & 15 deletions tools/src/main/java/org/dishevelled/bio/tools/ExtractFastaKmers.java
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,9 @@ public final class ExtractFastaKmers implements Callable<Integer> {
private final File outputKmerFile;
private final String alphabet;
private final int kmerLength;
private final boolean includeNs;
private final int upstreamLength;
private final int downstreamLength;
static final String DEFAULT_ALPHABET = "dna";
private static final String USAGE = "dsh-extract-fasta-kmers [args]";

Expand All @@ -76,19 +79,29 @@ public final class ExtractFastaKmers implements Callable<Integer> {
* @param outputKmerFile output kmer file, if any
* @param alphabet input FASTA file alphabet { dna, protein }, if any
* @param kmerLength kmer length, must be at least 1
* @param lineWidth line width
* @param includeNs for DNA sequences, include kmers containing Ns
* @param upstreamLength upstream reference sequence length to include, default 0
* @param downstreamLength downstream reference sequence length to include, default 0
*/
public ExtractFastaKmers(final Path inputFastaPath,
final File outputKmerFile,
final String alphabet,
final int kmerLength) {
final int kmerLength,
final boolean includeNs,
final int upstreamLength,
final int downstreamLength) {

checkArgument(kmerLength > 1, "kmer length must be at least 1");
checkArgument(kmerLength >= 1, "kmer length must be at least 1");
checkArgument(upstreamLength >= 0, "upstream length must be at least 0");
checkArgument(downstreamLength >= 0, "downstream length must be at least 0");

this.inputFastaPath = inputFastaPath;
this.outputKmerFile = outputKmerFile;
this.alphabet = alphabet;
this.kmerLength = kmerLength;
this.includeNs = includeNs;
this.upstreamLength = upstreamLength;
this.downstreamLength = downstreamLength;
}


Expand All @@ -105,17 +118,45 @@ public Integer call() throws Exception {

if (sequence.length() > kmerLength) {
String name = sequence.getName();
int lastStart = Math.max(1, sequence.length() - kmerLength);

for (int start = 1; start <= lastStart; start++) {
int end = start + kmerLength;

writer.print(sequence.subStr(start, end));
writer.print("\t");
writer.print(name);
writer.print("\t");
// use 0-based coordinates
writer.println(start - 1);
// 0-based half-open coordinates
int lastStart = Math.max(0, sequence.length() - kmerLength);
for (int start = 0; start <= lastStart; start++) {

// 1-based fully closed coordinates
int kmerStart = start + 1;
int kmerEnd = start + kmerLength;
String kmer = sequence.subStr(kmerStart, kmerEnd);

if (includeNs || !kmer.contains("n")) {
writer.print(kmer);
writer.print("\t");
writer.print(name);
writer.print("\t");

// output 0-based half-open coordinates
writer.print(start);

if (upstreamLength > 0) {
// 1-based fully closed coordinates
int upstreamStart = Math.max(1, start - upstreamLength);
int upstreamEnd = start;
writer.print("\t");
if (upstreamEnd >= upstreamStart) {
writer.print(sequence.subStr(upstreamStart, upstreamEnd));
}
}
if (downstreamLength > 0) {
// 1-based fully closed coordinates
int downstreamStart = Math.min(kmerEnd + 1, sequence.length() + 1);
int downstreamEnd = Math.min(kmerEnd + downstreamLength, sequence.length());
writer.print("\t");
if (downstreamEnd >= downstreamStart) {
writer.print(sequence.subStr(downstreamStart, downstreamEnd));
}
}
writer.print("\n");
}
}
}
}
Expand Down Expand Up @@ -149,14 +190,26 @@ boolean isProteinAlphabet() {
* @param args command line args
*/
public static void main(final String[] args) {

// install a signal handler to exit on SIGPIPE
sun.misc.Signal.handle(new sun.misc.Signal("PIPE"), new sun.misc.SignalHandler() {
@Override
public void handle(final sun.misc.Signal signal) {
System.exit(0);
}
});

Switch about = new Switch("a", "about", "display about message");
Switch help = new Switch("h", "help", "display help message");
PathArgument inputFastaPath = new PathArgument("i", "input-fasta-path", "input FASTA path, default stdin", false);
FileArgument outputKmerFile = new FileArgument("o", "output-kmer-file", "output kmer file, default stdout", false);
StringArgument alphabet = new StringArgument("e", "alphabet", "input FASTA alphabet { dna, protein }, default dna", false);
IntegerArgument kmerLength = new IntegerArgument("k", "kmer-length", "kmer length", true);
Switch includeNs = new Switch("n", "include-ns", "for DNA sequences, include kmers containing Ns");
IntegerArgument upstreamLength = new IntegerArgument("u", "upstream-length", "upstream length, default 0", false);
IntegerArgument downstreamLength = new IntegerArgument("d", "downstream-length", "downstream length, default 0", false);

ArgumentList arguments = new ArgumentList(about, help, inputFastaPath, outputKmerFile, alphabet, kmerLength);
ArgumentList arguments = new ArgumentList(about, help, inputFastaPath, outputKmerFile, alphabet, kmerLength, includeNs, upstreamLength, downstreamLength);
CommandLine commandLine = new CommandLine(args);

ExtractFastaKmers extractFastaKmers = null;
Expand All @@ -171,7 +224,7 @@ public static void main(final String[] args) {
Usage.usage(USAGE, null, commandLine, arguments, System.out);
System.exit(0);
}
extractFastaKmers = new ExtractFastaKmers(inputFastaPath.getValue(), outputKmerFile.getValue(), alphabet.getValue(DEFAULT_ALPHABET), kmerLength.getValue());
extractFastaKmers = new ExtractFastaKmers(inputFastaPath.getValue(), outputKmerFile.getValue(), alphabet.getValue(DEFAULT_ALPHABET), kmerLength.getValue(), includeNs.wasFound(), upstreamLength.getValue(0), downstreamLength.getValue(0));
}
catch (CommandLineParseException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
Expand Down

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