CRISPR-Cas9 Spring Batch Application
// This application models the CRISPR-Cas9 gene-editing process as a Spring Batch job.
// The genome is treated as a list of DNA base pairs, and the editing process is a batch job
// that reads, processes, and "writes" changes to that data.
import org.springframework.batch.core.Job;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.item.ItemProcessor;
import org.springframework.batch.item.ItemReader;
import org.springframework.batch.item.ItemWriter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import java.util.List;
import java.util.LinkedList;
import java.util.concurrent.atomic.AtomicInteger;
// Main entry point for the Spring Boot application
@SpringBootApplication
public class CrisprCas9Application {
public static void main(String[] args) {
SpringApplication.run(CrisprCas9Application.class, args);
}
}
/**
* Represents a segment of DNA with its sequence and location.
*/
record DnaSequence(String sequence, long location) {}
/**
* Represents a processed DNA sequence after the editing action.
*/
record EditedDnaSequence(long location, String originalSequence, String editedSequence, EditAction action) {}
/**
* Defines the type of gene-editing action.
*/
enum EditAction {
KNOCK_OUT, // Simulates deleting a gene or sequence
KNOCK_IN // Simulates inserting a new gene or sequence
}
/**
* Main Job Configuration for the CRISPR-Cas9 batch process.
* This class defines the overall job and its single step.
*/
@Configuration
@EnableBatchProcessing
class CrisprCas9BatchConfig {
@Autowired
private JobBuilderFactory jobBuilderFactory;
@Autowired
private StepBuilderFactory stepBuilderFactory;
// Defines the entire CRISPR-Cas9 job
@Bean
public Job crisprCas9Job(Step geneEditingStep) {
return jobBuilderFactory.get("crisprCas9Job")
.start(geneEditingStep)
.build();
}
// A single step representing the gene-editing process.
// This step combines the reader, processor, and writer.
@Bean
public Step geneEditingStep(
ItemReader<DnaSequence> reader,
ItemProcessor<DnaSequence, EditedDnaSequence> processor,
ItemWriter<EditedDnaSequence> writer
) {
return stepBuilderFactory.get("geneEditingStep")
.<DnaSequence, EditedDnaSequence>chunk(10) // Process 10 base pairs at a time
.reader(reader)
.processor(processor)
.writer(writer)
.build();
}
@Bean
public ItemReader<DnaSequence> genomeItemReader() {
return new GenomeItemReader("GATC", "GATTACAAGATCGATTACGGACATTAGATC");
}
@Bean
public ItemProcessor<DnaSequence, EditedDnaSequence> dnaSequenceProcessor() {
return new DnaSequenceProcessor(EditAction.KNOCK_IN, "GCTACGC");
}
@Bean
public ItemWriter<EditedDnaSequence> genomeItemWriter() {
return new GenomeItemWriter();
}
}
/**
* ItemReader: The Guide RNA (gRNA)
* This component reads chunks of the conceptual "genome" and is "guided" by a target sequence.
*/
class GenomeItemReader implements ItemReader<DnaSequence> {
// A simple conceptual "genome" string to read from
private final String genome;
private final String targetSequence;
private final AtomicInteger pointer = new AtomicInteger(0);
public GenomeItemReader(String targetSequence, String genome) {
this.targetSequence = targetSequence;
this.genome = genome;
System.out.println("Guide RNA initialized. Target sequence: " + targetSequence);
}
@Override
public DnaSequence read() {
if (pointer.get() >= genome.length()) {
return null; // End the job
}
// Search for the target sequence from the current pointer position
int startIndex = genome.indexOf(targetSequence, pointer.get());
if (startIndex == -1) {
System.out.println("Target sequence not found. Job finished.");
pointer.set(genome.length()); // Ensure the job ends
return null;
}
// Found the target. Return the DNA sequence chunk containing the target.
// We return the target itself for simplicity.
pointer.set(startIndex + targetSequence.length());
System.out.printf("Guide RNA found target at location %d. Passing to Cas9.\n", startIndex);
return new DnaSequence(targetSequence, startIndex);
}
}
/**
* ItemProcessor: The Cas9 Protein
* This component acts as the molecular scissors, performing the specified edit action.
*/
class DnaSequenceProcessor implements ItemProcessor<DnaSequence, EditedDnaSequence> {
private final EditAction editAction;
private final String newSequence;
public DnaSequenceProcessor(EditAction editAction, String newSequence) {
this.editAction = editAction;
this.newSequence = newSequence;
System.out.println("Cas9 Protein initialized. Edit action: " + editAction);
}
@Override
public EditedDnaSequence process(DnaSequence dna) {
System.out.printf("Cas9 is processing sequence '%s' at location %d...\n", dna.sequence(), dna.location());
String editedContent = switch (editAction) {
case KNOCK_OUT -> "---"; // Simulate deletion
case KNOCK_IN -> newSequence; // Simulate insertion
};
System.out.printf("Cas9 completed edit. New sequence: %s\n", editedContent);
return new EditedDnaSequence(dna.location(), dna.sequence(), editedContent, editAction);
}
}
/**
* ItemWriter: The Cellular Repair Mechanism
* This component takes the edited DNA and "writes" it back into the genome.
*/
class GenomeItemWriter implements ItemWriter<EditedDnaSequence> {
private final List<String> genomeState = new LinkedList<>();
public GenomeItemWriter() {
// Initialize with a simple representation of the genome
for (char c : "GATTACAAGATCGATTACGGACATTAGATC".toCharArray()) {
genomeState.add(String.valueOf(c));
}
}
@Override
public void write(List<? extends EditedDnaSequence> editedDnaSequences) {
System.out.println("Cellular repair mechanism is starting to write edits...");
for (EditedDnaSequence editedDna : editedDnaSequences) {
long start = editedDna.location();
long end = start + editedDna.originalSequence().length();
// Simulate the repair process by modifying the in-memory genome
// This is a simplified representation of DNA repair
for (long i = start; i < end; i++) {
if (i < genomeState.size()) {
genomeState.set((int) i, "[EDITED]");
}
}
if (editedDna.action() == EditAction.KNOCK_IN) {
// For simplicity, we just print the insertion
System.out.printf("Inserted '%s' at location %d.\n", editedDna.editedSequence(), editedDna.location());
}
System.out.printf("Repair complete at location %d. Final state is conceptual.\n", editedDna.location());
}
System.out.println("Cellular repair complete for this chunk.");
}
}
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