The definitive Explanation on how Spring Batch could may explain How Crispr cas9 Works

 The definitive Explanation on how Spring Batch could may explain How Crispr cas9 Works

Author : Wadï Mami

Date : 16/01/2023

Email : wmami@steg.com.tn / didipostman77@gmail.com


Abstract

Many people were not convinced about how Spring Batch could may explain how CRISPR Cas9 Works. In this following paper I will try to represent the Howto in more details with some changes to fit how CRISPR Cas9 Works as We will have 2 batchs one batch job for creating the CRISPR Arrays with input virus DNA data/DNA.csv and output the CRISPR Arrays in outputFile.csv . And the second Batch is the second phase disabling the virus by using input the CRISPR Arrays outputFile.csv and altering the virus DNA data/DNA.csv 


The CRISPR arrays :

Spring Batch reads and process DNA sequentially until reaching commit-interval value then it writes transformed items (DNA) simultaneously.

Spring Batch is the bacteria


The bacteria capture snippets of DNA from invading viruses and use them to create DNA segments known as CRISPR arrays

 example private String dna_pattern = "AATTCC"; //snippets of DNA from invading viruses in

 https://github.com/didipostman/CrisprCas9/blob/main/src/main/java/com/juxtapose/example/ch02/DNA_SequenceProcessor.java

<=> Spring Batch read DNA file or DNA database , The DNA file or the DNA database are Viruses DNA.

 SpringBatch read() --->ItemReader and ItemReader return item. <=> Spring Batch process() ----> ItemProcessor and

 return transformed item = DNA segments known as CRISPR arrays Here I use DNA_sequenceProcessor class that

 implements ItemProcessor and uses Karp Rabin (you can use other DNA pattern recognition algorithm)

Below is a code representation of the same concepts shown above

List items = new Arraylist();

for(int i = 0; i < commitInterval; i++){

    Object item = itemReader.read()

    Object processedItem = itemProcessor.process(item);

    items.add(processedItem);

}

itemWriter.write(items);

The following code fragment shows how to define a CRISPR ARRAYS step in XML:

<job id="dnaSeq">

        <step id="CRISPR_ARRAYS">

            <tasklet transaction-manager="transactionManager">

                <chunk reader="csvItemReader" writer="csvItemWriter"

                    processor="DNA_SequenceProcessor" commit-interval="2">

                </chunk>

            </tasklet>

        </step>

 </job>

<bean:bean id="csvItemReader"

        class="org.springframework.batch.item.file.FlatFileItemReader"

        scope="step">

        <bean:property name="resource"

            value="classpath:ch02/data/DNA.csv"/>

        <bean:property name="lineMapper">

            <bean:bean

                class="org.springframework.batch.item.file.mapping.DefaultLineMapper">

                <bean:property name="lineTokenizer" ref="lineTokenizer"/>

                <bean:property name="fieldSetMapper">

                    <bean:bean class="org.springframework.batch.item.file.mapping.BeanWrapperFieldSetMapper">

                        <bean:property name="prototypeBeanName" value="DNA_Sequence">

                        </bean:property>

                    </bean:bean>

                </bean:property>

            </bean:bean>

        </bean:property>

  </bean:bean>

    <!-- lineTokenizer -->

    <bean:bean id="lineTokenizer"

        class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer">

        <bean:property name="delimiter" value=","/>

        <bean:property name="names">

            <bean:list>

                <bean:value>dna</bean:value>

             <bean:value>crissprArrays</bean:value>

               

            </bean:list>

        </bean:property>

    </bean:bean>

   

   

    <bean:bean id="csvItemWriter"

        class="org.springframework.batch.item.file.FlatFileItemWriter"

        scope="step">

        <bean:property name="resource" value="file:target/ch02/outputFile.csv"/>

        <bean:property name="lineAggregator">

            <bean:bean

                class="org.springframework.batch.item.file.transform.DelimitedLineAggregator">

                <bean:property name="delimiter" value="|"></bean:property>

                <bean:property name="fieldExtractor">

                    <bean:bean

                        class="org.springframework.batch.item.file.transform.BeanWrapperFieldExtractor">

                        <bean:property name="names"

                             value="dna,crissprArrays">

                        </bean:property>

                    </bean:bean>

                </bean:property>

            </bean:bean>

        </bean:property>

    </bean:bean>

 

I hope you figured out the nuance on how Spring Batch create CRISPR Arrays in outputFile.csv

The 2nd Phase disabling the viruses another Batch process:

The CRISPR arrays allow the bacteria to "remember" the viruses (or closely related ones). If the viruses attack again,

 the bacteria produce RNA segments from the CRISPR arrays to target the viruses

The bacteria (Spring Batch)  then use Cas9 or a similar enzyme to cut the DNA apart, which disables the virus.

 <=> Spring batch write(transformed items) ----> ItemWriter ( cut Virus DNA ). 

It is another Batch where the reader reads precedent outputFile.csv (CRISPR arrays) and cut simultaneously the virus. 



<step id="step2">

        <tasklet transaction-manager="transactionManager">

            <chunk reader="itemReader" writer="itemWriter" commit-interval="10"/>

        </tasklet>

    </step>

 

 

Conclusion

As You can see in this brief explanation what was done in only one batch step job previously  is divided into 2 batch job each job with one step the first batch job step creates the CRISPR Arrays. And the second batch job step is the second phase disabling the viruses simultaneously after reading CRISPR ARRAYS file outputFile.csv and altering the viruses DNA file write(items)

data/DNA.csv

Spring Batch + Karp Rabin = how CRISPR Cas9 works is my IT theoretical model may be it could be interesting and useful for drugs discovery. The model is an idea that had been haunting me since 2012. I share it with you. I can’t go further with it, may be you find it useful interesting and continue developement. The model is under MIT License

 https://github.com/didipostman/CrisprCas9


If the Theory model is wrong or unseful or uninteresting read below there is always something to win from this idea as https://www.tudelft.nl/en/2018/tu-delft/mathematics-explains-why-crispr-cas9-sometimes-cuts-the-wrong-dna

Processing large volume of data has always been a major problem due to the increasing volume of the data. Batch processing can be applied in many use cases. Among them why not Pattern Matching for DNA Sequencing Data. Spring Batch provides functions for processing large volumes of data in batch jobs. In our case reading DNA file or database table and seeking for patterns I mean all the locations of the specified pattern inside a DNA sequence.

Spring batch to process huge data : Spring Batch is a lightweight, comprehensive batch framework designed to enable the development of robust batch applications vital for the daily operations of enterprise systems.

Conclusion

DNA is a sequence of letters such as A, C, G, T. Searching for specific sequences is often difficult due to measurement errors, mutations or evolutionary alterations. Thus, similarity of two sequences using Levenshtein Distance is more useful than exact matches.

So instead of Karp Rabin we will use Levenshtein Distance or Jaro_Winkler_Similarity by using

Package org.apache.commons.text.similarity commons.apache.org/proper/commons-text/apid..

So

Spring Batch + Levenshtein Distance or Jaro_Winkler Similarity = How Crispr cas9 Works due to (https://www.tudelft.nl/en/2018/tu-delft/mathematics-explains-why-crispr-cas9-sometimes-cuts-the-wrong-dna)


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