opentreeoflife / pta

phylogeny-taxonomy alignment service

pta

A phylogeny-taxonomy alignment service for the Open Tree project.

The general idea is that the service receives a tree with leaves mapped to Open Tree Taxonomy (OTT) ids, and returns json data required for rendering the alignment of the tree as an interactive d3 graphic, e.g.:

http://reelab.net/phylografter/graph/view_ott/1

Installing

pta is a web2py app. This repo can be cloned directly into web2py's applications directory.

Requirements

• graph-tool and its dependencies
• ivy and its dependencies

(These may be tricky to install if you are not using Ubuntu.)

Usage

Start the server, which will listen on localhost port 8000 by default:

python ./web2py.py

As a web app

Basic functionality is available by visiting http://localhost:8000/pta

As a web service

Currently the service expects an entire study nexson file to be POSTed in a data parameter. For example to submit a file called ot_20.json:

curl --data-urlencode data@ot_20.json http://localhost:8000/pta/default/index.json

The response will be json data object with a key treeids mapping to a list (possibly empty) of tree id values corresponding to trees in the nexson file that were processed. The phylogeny-taxonomy alignment data for each tree can be retrieved from the json object using these tree ids as keys.

Caveats

• At present little if any sanity checking is done and informative error messages are nonexistent.

• Please note, the app process will use about 1.8 GB of RAM, because it keeps the entire Open Tree Taxonomy in memory. After launching the app, the first request to the service will be a bit slow as this is loaded.