CODEWITHSUNDEEP
pythonperformancesqlite
gunzapper
gunzapper

Reputation: 457

sqlite and python... fast and furious

I implemented in python a program that builds some db from protein fasta file. A fasta file is a text file that contains some macromolecular sequences. You can read more about here. From each protein my program generate a list of peptides, they are pieces of proteins. For my goals the program builds and interrogates a DB in SQLite.

Do you know if there are many tricks to populate or interrogate a sqlite db faster in python? If I use layers or ORMs like SQLAlchemy, can I improve the performance?

Upvotes: 4

Views: 2768

Answers (1)

Zach Kelling
Zach Kelling

Reputation: 53819

You won't improve performance, the ORM layer will add a bit of overhead, but you'll probably be able to experiment easier. Given the size of your data you might be able to create the database in memory which would be faster. Or you might want to look at a different type of database, like redis for example.

Upvotes: 4

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