Storing Matching Pairs of Numbers Efficiently in SQLite

Introduction

SQLite is a popular relational database management system that allows you to store and manage data efficiently. In this article, we will explore how to store matching pairs of numbers in an efficient manner using SQLite.

Problem Statement

We are given a table orthologs with the following structure:

The problem is to find all genes that form a pair between two taxons, say 25 and 37. We need to run two queries because we don’t know if the first value of the pair is in the taxon1 column or the taxon2 column.

Current Solution

The current solution involves running two separate queries:

SELECT taxon1, gene1, taxon2, gene2 
FROM orthologs 
WHERE taxon1=25 AND taxon2=37

SELECT taxon2, gene2, taxon1, gene1 
FROM orthologs 
WHERE taxon2=25 AND taxon1=37

This approach is inefficient because it requires two separate queries to find all genes that form a pair between two taxons.

Solution 1: Using MIN() and MAX()

We can use the MIN() and MAX() functions in SQLite to solve this problem. The idea is to find the minimum and maximum values of both pairs of taxon and gene IDs.

SELECT taxon1, gene1, taxon2, gene2 
FROM orthologs 
WHERE MIN(taxon1, taxon2) = 25 AND MAX(taxon1, taxon2) = 37

This query will return all genes that form a pair between two taxons where the minimum value of both pairs is 25 and the maximum value of both pairs is 37.

Solution 2: Using IN Operator

Another approach is to use the IN operator with the ROW VALUES clause. This allows us to specify multiple values for each pair of taxon and gene IDs.

SELECT taxon1, gene1, taxon2, gene2 
FROM orthologs 
WHERE (taxon1, taxon2) IN((25, 37), (37, 25))

This query will return all genes that form a pair between two taxons where the first value of both pairs is either 25 or 37.

Solution 3: Using IN Operator with Multiple Pairs

We can also use the IN operator to specify multiple values for each pair of taxon and gene IDs. This allows us to find all genes that form a pair between two taxons where the first value of both pairs is either 25 or 37.

SELECT taxon1, gene1, taxon2, gene2 
FROM orthologs 
WHERE (taxon1, taxon2) IN((25, 37), (37, 25))

This query will return all genes that form a pair between two taxons where the first value of both pairs is either 25 or 37.

Solution 4: Finding Gene IDs for a Given Taxon ID

We can also use this approach to find gene IDs for a given taxon ID. We can specify multiple values for each pair of taxon and gene IDs, like so:

SELECT taxon1, gene1, taxon2, gene2 
FROM orthologs 
WHERE (taxon1, taxon2) IN((taxon_id, 123), (123, taxon_id))

This query will return all genes that form a pair between two taxons where the first value of both pairs is either the specified taxon ID or 123.

Conclusion

In this article, we explored how to store matching pairs of numbers in an efficient manner using SQLite. We discussed four different approaches: using MIN() and MAX(), using the IN operator with ROW VALUES, using the IN operator with multiple pairs, and finding gene IDs for a given taxon ID.

Each approach has its own advantages and disadvantages, and the choice of which one to use depends on the specific requirements of your application.

Last modified on 2023-12-24