Skip to main content

Generic tools to identify overlapping genomic regions

Project description

The intervalTree class is an adaptation of the interval tree algorithm based on red-black trees from Introduction to Algorithms by Cormen, Leiserson, Rivest and Stein (2001) 2nd Edition, The MIT Press

This makes a nice self-balancing tree. The alrogithm may be more efficient if items are randomly selected for insertion, instead of in sort order.

I’ve modified the CLRS algorithm to report all overlapping nodes instead of only the first node. This involved adding a min value instead of only a max value in order to speed up the search by checking if the subtree min,max overlaps with the search interval. The search routine is also recursive.

Project details


Release history Release notifications

This version
History Node

0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
murphy-0.1.zip (26.1 kB) Copy SHA256 hash SHA256 Source None Jul 16, 2017

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page