Programmatic Access to the Alignment Server

alignment_server_access.py

import time
import requests

FINISHED = set(['succeeded', 'failed'])


# Some large and slow requests may fail because of the retry limit in requests.
# Set the retry higher for these cases.
# 3 seconds is a pretty good wait most requests should be done in < 10 seconds.
def fetch(*args, **kwargs):
    response = requests.get(*args, **kwargs)
    response.raise_for_status()
    data = response.json()
    while data['status'] not in FINISHED:
        time.sleep(3)
        response = requests.get(*args, **kwargs)
        data = response.json()
    return response

# Returned content type may be set by changing the accept
headers = {'Accept': 'application/json'}

# Access variations for one nucleotide
response = fetch("http://rna.bgsu.edu/r3d-2-msa",
                 params={'units': '2AW7|1|A|A|887'}, headers=headers)
data = response.json()

# Access variations while omitting the base letter
response = fetch("http://rna.bgsu.edu/r3d-2-msa",
                 params={'units': '2AW7|1|A||887'}, headers=headers)
data = response.json()

# Access variations for a range of nucleotides
# We can also use a format parameter to set the returned content type
response = fetch("http://rna.bgsu.edu/r3d-2-msa",
                 params={'units': '2AW7|1|A|A|887:2AW7|1|A|A|895', 'format': 'json'})
data = response.json()

# Access variations for multiple ranges
response = fetch("http://rna.bgsu.edu/r3d-2-msa",
                 params={'units': '2AW7|1|A|A|887:2AW7|1|A|A|895,2AW7|1|A|G|200:2AW7|1|A|C|210', 'format': 'json'})
data = response.json()

# It is possible to have up to 5 ranges in the list of ranges