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Added task 3475
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‎src/main/kotlin/g3401_3500/s3475_dna_pattern_recognition/readme.md

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3475\. DNA Pattern Recognition
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Medium
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Table: `Samples`
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+----------------+---------+
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| Column Name | Type |
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+----------------+---------+
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| sample_id | int |
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| dna_sequence | varchar |
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| species | varchar |
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+----------------+---------+
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sample_id is the unique key for this table.
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Each row contains a DNA sequence represented as a string of characters (A, T, G, C) and the species it was collected from.
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Biologists are studying basic patterns in DNA sequences. Write a solution to identify `sample_id` with the following patterns:
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* Sequences that **start** with **ATG** (a common **start codon**)
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* Sequences that **end** with either **TAA**, **TAG**, or **TGA** (**stop codons**)
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* Sequences containing the motif **ATAT** (a simple repeated pattern)
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* Sequences that have **at least** `3` **consecutive** **G** (like **GGG** or **GGGG**)
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Return _the result table ordered by __sample\_id in **ascending** order_.
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The result format is in the following example.
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**Example:**
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**Input:**
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Samples table:
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+-----------+------------------+-----------+
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| sample_id | dna_sequence | species |
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+-----------+------------------+-----------+
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| 1 | ATGCTAGCTAGCTAA | Human |
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| 2 | GGGTCAATCATC | Human |
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| 3 | ATATATCGTAGCTA | Human |
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| 4 | ATGGGGTCATCATAA | Mouse |
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| 5 | TCAGTCAGTCAG | Mouse |
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| 6 | ATATCGCGCTAG | Zebrafish |
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| 7 | CGTATGCGTCGTA | Zebrafish |
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+-----------+------------------+-----------+
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**Output:**
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+-----------+------------------+-------------+-------------+------------+------------+------------+
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| sample_id | dna_sequence | species | has_start | has_stop | has_atat | has_ggg |
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+-----------+------------------+-------------+-------------+------------+------------+------------+
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| 1 | ATGCTAGCTAGCTAA | Human | 1 | 1 | 0 | 0 |
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| 2 | GGGTCAATCATC | Human | 0 | 0 | 0 | 1 |
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| 3 | ATATATCGTAGCTA | Human | 0 | 0 | 1 | 0 |
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| 4 | ATGGGGTCATCATAA | Mouse | 1 | 1 | 0 | 1 |
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| 5 | TCAGTCAGTCAG | Mouse | 0 | 0 | 0 | 0 |
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| 6 | ATATCGCGCTAG | Zebrafish | 0 | 1 | 1 | 0 |
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| 7 | CGTATGCGTCGTA | Zebrafish | 0 | 0 | 0 | 0 |
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+-----------+------------------+-------------+-------------+------------+------------+------------+
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**Explanation:**
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* Sample 1 (ATGCTAGCTAGCTAA):
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* Starts with ATG (has\_start = 1)
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* Ends with TAA (has\_stop = 1)
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* Does not contain ATAT (has\_atat = 0)
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* Does not contain at least 3 consecutive 'G's (has\_ggg = 0)
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* Sample 2 (GGGTCAATCATC):
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* Does not start with ATG (has\_start = 0)
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* Does not end with TAA, TAG, or TGA (has\_stop = 0)
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* Does not contain ATAT (has\_atat = 0)
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* Contains GGG (has\_ggg = 1)
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* Sample 3 (ATATATCGTAGCTA):
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* Does not start with ATG (has\_start = 0)
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* Does not end with TAA, TAG, or TGA (has\_stop = 0)
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* Contains ATAT (has\_atat = 1)
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* Does not contain at least 3 consecutive 'G's (has\_ggg = 0)
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* Sample 4 (ATGGGGTCATCATAA):
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* Starts with ATG (has\_start = 1)
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* Ends with TAA (has\_stop = 1)
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* Does not contain ATAT (has\_atat = 0)
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* Contains GGGG (has\_ggg = 1)
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* Sample 5 (TCAGTCAGTCAG):
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* Does not match any patterns (all fields = 0)
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* Sample 6 (ATATCGCGCTAG):
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* Does not start with ATG (has\_start = 0)
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* Ends with TAG (has\_stop = 1)
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* Starts with ATAT (has\_atat = 1)
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* Does not contain at least 3 consecutive 'G's (has\_ggg = 0)
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* Sample 7 (CGTATGCGTCGTA):
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* Does not start with ATG (has\_start = 0)
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* Does not end with TAA, "TAG", or "TGA" (has\_stop = 0)
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* Does not contain ATAT (has\_atat = 0)
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* Does not contain at least 3 consecutive 'G's (has\_ggg = 0)
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**Note:**
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* The result is ordered by sample\_id in ascending order
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* For each pattern, 1 indicates the pattern is present and 0 indicates it is not present

‎src/main/kotlin/g3401_3500/s3475_dna_pattern_recognition/script.sql

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# Write your MySQL query statement below
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# #Medium #2025_03_04_Time_645_ms_(100.00%)_Space_0.0_MB_(100.00%)
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WITH SampleAnalysisCte AS (
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SELECT sample_id, dna_sequence, species,
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dna_sequence REGEXP '^ATG' AS has_start,
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dna_sequence REGEXP 'TAA$|TAG$|TGA$' AS has_stop,
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dna_sequence REGEXP '.*ATAT.*' AS has_atat,
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dna_sequence REGEXP '.*GGG.*' AS has_ggg
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FROM Samples
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)
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SELECT * FROM SampleAnalysisCte
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ORDER BY sample_id;

‎src/test/kotlin/g3401_3500/s3475_dna_pattern_recognition/MysqlTest.kt

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package g3401_3500.s3475_dna_pattern_recognition
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import org.hamcrest.CoreMatchers.equalTo
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import org.hamcrest.MatcherAssert.assertThat
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import org.junit.jupiter.api.Test
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import org.zapodot.junit.db.annotations.EmbeddedDatabase
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import org.zapodot.junit.db.annotations.EmbeddedDatabaseTest
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import org.zapodot.junit.db.common.CompatibilityMode
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import java.io.BufferedReader
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import java.io.FileNotFoundException
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import java.io.FileReader
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import java.sql.SQLException
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import java.util.stream.Collectors
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import javax.sql.DataSource
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@EmbeddedDatabaseTest(
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compatibilityMode = CompatibilityMode.MySQL,
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initialSqls = [
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(
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" CREATE TABLE Samples (" +
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" sample_id INT," +
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" dna_sequence VARCHAR(100)," +
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" species VARCHAR(100)" +
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");" +
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"insert into Samples (sample_id, dna_sequence, species) values " +
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"(1, 'ATGCTAGCTAGCTAA', 'Human');" +
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"insert into Samples (sample_id, dna_sequence, species) values " +
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"(2, 'GGGTCAATCATC', 'Human');" +
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"insert into Samples (sample_id, dna_sequence, species) values " +
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"(3, 'ATATATCGTAGCTA', 'Human');" +
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"insert into Samples (sample_id, dna_sequence, species) values " +
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"(4, 'ATGGGGTCATCATAA', 'Human');" +
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"insert into Samples (sample_id, dna_sequence, species) values " +
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"(5, 'TCAGTCAGTCAG', 'Human');" +
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"insert into Samples (sample_id, dna_sequence, species) values " +
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"(6, 'ATATCGCGCTAG', 'Zebrafish');" +
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"insert into Samples (sample_id, dna_sequence, species) values " +
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"(7, 'CGTATGCGTCGTA', 'Zebrafish');"
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),
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],
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)
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internal class MysqlTest {
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@Test
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@Throws(SQLException::class, FileNotFoundException::class)
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fun testScript(@EmbeddedDatabase dataSource: DataSource) {
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dataSource.connection.use { connection ->
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connection.createStatement().use { statement ->
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statement.executeQuery(
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BufferedReader(
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FileReader(
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(
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"src/main/kotlin/g3401_3500/" +
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"s3475_dna_pattern_recognition/" +
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"script.sql"
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),
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),
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)
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.lines()
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.collect(Collectors.joining("\n"))
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.replace("#.*?\\r?\\n".toRegex(), ""),
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).use { resultSet ->
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(true))
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assertThat<String>(resultSet.getNString(1), equalTo<String>("1"))
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assertThat<String>(
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resultSet.getNString(2),
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equalTo<String>("ATGCTAGCTAGCTAA"),
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)
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assertThat<String>(resultSet.getNString(3), equalTo<String>("Human"))
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assertThat<String>(resultSet.getNString(4), equalTo<String>("TRUE"))
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assertThat<String>(resultSet.getNString(5), equalTo<String>("TRUE"))
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assertThat<String>(resultSet.getNString(6), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(7), equalTo<String>("FALSE"))
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(true))
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assertThat<String>(resultSet.getNString(1), equalTo<String>("2"))
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assertThat<String>(
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resultSet.getNString(2),
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equalTo<String>("GGGTCAATCATC"),
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)
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assertThat<String>(resultSet.getNString(3), equalTo<String>("Human"))
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assertThat<String>(resultSet.getNString(4), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(5), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(6), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(7), equalTo<String>("TRUE"))
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(true))
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assertThat<String>(resultSet.getNString(1), equalTo<String>("3"))
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assertThat<String>(
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resultSet.getNString(2),
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equalTo<String>("ATATATCGTAGCTA"),
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)
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assertThat<String>(resultSet.getNString(3), equalTo<String>("Human"))
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assertThat<String>(resultSet.getNString(4), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(5), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(6), equalTo<String>("TRUE"))
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assertThat<String>(resultSet.getNString(7), equalTo<String>("FALSE"))
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(true))
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assertThat<String>(resultSet.getNString(1), equalTo<String>("4"))
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assertThat<String>(
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resultSet.getNString(2),
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equalTo<String>("ATGGGGTCATCATAA"),
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)
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assertThat<String>(resultSet.getNString(3), equalTo<String>("Human"))
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assertThat<String>(resultSet.getNString(4), equalTo<String>("TRUE"))
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assertThat<String>(resultSet.getNString(5), equalTo<String>("TRUE"))
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assertThat<String>(resultSet.getNString(6), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(7), equalTo<String>("TRUE"))
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(true))
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assertThat<String>(resultSet.getNString(1), equalTo<String>("5"))
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assertThat<String>(
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resultSet.getNString(2),
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equalTo<String>("TCAGTCAGTCAG"),
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)
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assertThat<String>(resultSet.getNString(3), equalTo<String>("Human"))
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assertThat<String>(resultSet.getNString(4), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(5), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(6), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(7), equalTo<String>("FALSE"))
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(true))
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assertThat<String>(resultSet.getNString(1), equalTo<String>("6"))
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assertThat<String>(
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resultSet.getNString(2),
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equalTo<String>("ATATCGCGCTAG"),
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)
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assertThat<String>(
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resultSet.getNString(3),
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equalTo<String>("Zebrafish"),
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)
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assertThat<String>(resultSet.getNString(4), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(5), equalTo<String>("TRUE"))
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assertThat<String>(resultSet.getNString(6), equalTo<String>("TRUE"))
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assertThat<String>(resultSet.getNString(7), equalTo<String>("FALSE"))
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(true))
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assertThat<String>(resultSet.getNString(1), equalTo<String>("7"))
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assertThat<String>(
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resultSet.getNString(2),
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equalTo<String>("CGTATGCGTCGTA"),
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)
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assertThat<String>(
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resultSet.getNString(3),
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equalTo<String>("Zebrafish"),
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)
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assertThat<String>(resultSet.getNString(4), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(5), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(6), equalTo<String>("FALSE"))
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assertThat<String>(resultSet.getNString(7), equalTo<String>("FALSE"))
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assertThat<Boolean>(resultSet.next(), equalTo<Boolean>(false))
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}
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}
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}
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}
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}

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