A sample script for downloading RNA 3D Motif Atlas entries.

motif_download.py

"""

A sample python script for downloading Motif Atlas entries from
the RNA 3D Motif Atlas (http://rna.bgsu.edu/rna3dhub/motifs).

Usage:
python motif_download.py

"""

import urllib2
import json

url = 'http://rna.bgsu.edu/rna3dhub/motif/view/IL_85647.1/json'

json_data = urllib2.urlopen(url).read()
motif = json.loads(json_data)

print 'Motif id: %s'           % motif['motif_id']
print 'Common name: %s'        % motif['common_name']
print 'Annotation: %s'         % motif['annotation']
print 'Basepair signature: %s' % motif['bp_signature']
print '%s instances'           % motif['num_instances']
print '%s nucleotides'         % motif['num_nucleotides']

for loop_id, nts in motif['alignment'].iteritems():
    print 'Loop id %s' % loop_id
    print nts