annotate get_sequences.py @ 7:c79ce2342f1e draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322

# A simple tool to connect to the Ensembl server and retrieve sequences using
# the Ensembl REST API.
import json
import optparse
from itertools import islice
from urllib.parse import urljoin

import requests

parser = optparse.OptionParser()
parser.add_option("-i", "--input", help="List of Ensembl IDs")

parser.add_option(
    "-t",
    "--type",
    type="choice",
    choices=["genomic", "cds", "cdna", "protein"],
    default="genomic",
    help="Type of sequence",
)
parser.add_option(
    "--expand_3prime",
    type="int",
    default=0,
    help="Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type",
)
parser.add_option(
    "--expand_5prime",
    type="int",
    default=0,
    help="Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type",
)
options, args = parser.parse_args()
if options.input is None:
    raise Exception("-i option must be specified")

server = "https://rest.ensembl.org"
ext = "sequence/id"

headers = {"Content-Type": "text/x-fasta", "Accept": "text/x-fasta"}
params = {
    k: getattr(options, k) for k in ("type", "expand_3prime", "expand_5prime")
}
with open(options.input) as f:
    # Need to split the file in chunks of 50 lines because of the limit imposed by Ensembl
    while True:
        ids = [line.strip() for line in islice(f, 50)]
        if not ids:
            break
        data = {"ids": ids}
        r = requests.post(
            urljoin(server, ext),
            params=params,
            headers=headers,
            data=json.dumps(data),
            allow_redirects=False,
        )

        if not r.ok:
            r.raise_for_status()

        print(r.text)