Mercurial > repos > earlhaminst > ensembl_get_sequences

comparison get_feature_info.py @ 7:c79ce2342f1e draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
author earlhaminst
date Mon, 17 Feb 2025 14:49:24 +0000
parents 7af66c2b3831
children
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6:7af66c2b3831 7:c79ce2342f1e
1 # A simple tool to connect to the Ensembl server and retrieve feature 1 # A simple tool to connect to the Ensembl server and retrieve feature
2 # information using the Ensembl REST API. 2 # information using the Ensembl REST API.
3 from __future__ import print_function
4
5 import json 3 import json
6 import optparse 4 import optparse
7 from itertools import islice 5 from itertools import islice
6 from urllib.parse import urljoin
8 7
9 import requests 8 import requests
10 from six.moves.urllib.parse import urljoin
11 9
12 parser = optparse.OptionParser() 10 parser = optparse.OptionParser()
13 parser.add_option('-i', '--input', help='List of Ensembl IDs') 11 parser.add_option("-i", "--input", help="List of Ensembl IDs")
14 parser.add_option('-e', '--expand', type='choice', choices=['0', '1'], 12 parser.add_option(
15 default='0', 13 "-e",
16 help='Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well.') 14 "--expand",
15 type="choice",
16 choices=["0", "1"],
17 default="0",
18 help="Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well.",
19 )
17 20
18 parser.add_option('-f', '--format', type='choice', 21 parser.add_option(
19 choices=['full', 'condensed'], default='full', 22 "-f",
20 help='Specify the formats to emit from this endpoint') 23 "--format",
24 type="choice",
25 choices=["full", "condensed"],
26 default="full",
27 help="Specify the formats to emit from this endpoint",
28 )
21 options, args = parser.parse_args() 29 options, args = parser.parse_args()
22 if options.input is None: 30 if options.input is None:
23 raise Exception('-i option must be specified') 31 raise Exception("-i option must be specified")
24 32
25 33
26 server = 'https://rest.ensembl.org' 34 server = "https://rest.ensembl.org"
27 ext = 'lookup/id' 35 ext = "lookup/id"
28 36
29 headers = {'Content-Type': 'application/json', 'Accept': 'application/json'} 37 headers = {"Content-Type": "application/json", "Accept": "application/json"}
30 params = dict((k, getattr(options, k)) for k in ['format', 'expand']) 38 params = {k: getattr(options, k) for k in ("format", "expand")}
31 39
32 first = True 40 first = True
33 41
34 print('{') 42 print("{")
35 43
36 with open(options.input) as f: 44 with open(options.input) as f:
37 while True: 45 while True:
38 ids = [line.strip() for line in islice(f, 50)] 46 ids = [line.strip() for line in islice(f, 50)]
39 if not ids: 47 if not ids:
40 break 48 break
41 if not first: 49 if not first:
42 print(",") 50 print(",")
43 data = {'ids': ids} 51 data = {"ids": ids}
44 r = requests.post(urljoin(server, ext), params=params, headers=headers, 52 r = requests.post(
45 data=json.dumps(data), allow_redirects=False) 53 urljoin(server, ext),
54 params=params,
55 headers=headers,
56 data=json.dumps(data),
57 allow_redirects=False,
58 )
46 59
47 if not r.ok: 60 if not r.ok:
48 r.raise_for_status() 61 r.raise_for_status()
49 62
50 print(r.text[1:-1]) 63 print(r.text[1:-1])
51 64
52 first = False 65 first = False
53 66
54 print('}') 67 print("}")