Post tagged: database


A builder for more compact REDCap schema


REDCap is a fabulously useful tool for creating web databases, including a useful scheme for defining the database schema ("data dictionaries") in plain CSV files. However, difficulties arise when designing complex schema. It is cumbersome to code multiuple occurences of essentially the same field (e.g. sample_1 ... sample_2 ...). If …


Viral nervous necrosis (VNN) is a severe neuropathological disease affecting a broad variety of finfish species worldwide. The causative agent of VNN is a small virus with a bi-segmented RNA genome known as betanodavirus. At least four genotypes with distinct, but yet insufficiently characterized, epidemiological features are recognized. The …

(Re-)building databases with csvsql

Tips and traps when going from a database dump to a database

The scenario

You have a bunch of related CSV files.

Maybe they're the result of a raw database dump. Maybe they've been generated in some other way: experimental results, various public data sets, whatever. But the important thing is that you need to make a database from them. Perhaps because …

SQLAlchemy merge and relations

In which an oddity in SQLAlchemy is spotted, and it turns out to be a bug not a misunderstanding.


The merge function in SQLAlchemy lets an object seem to get pushed to the database, but actually stores and returns a copy of the object. This is handy for when …

Fetch sequences from db

A simple script to grab bioseqs by accession.

This just wraps the BioRuby fetch functionality in a friendly commandline interface. In brief, it can accept accession ids on the commandline or from a piped file (one accession per line) and save the corresponding sequences from the db. Sequences may be downloaded via the bioruby or EBI servers. The …