Mercurial > repos > jjohnson > ensembl_cdna_translate

comparison ensembl_rest.py @ 8:5c92d0be6514 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Thu, 14 Dec 2017 13:32:00 -0500
parents
children
comparison
equal deleted inserted replaced
7:d59e3ce10e74 8:5c92d0be6514
1 #!/usr/bin/env python
2 """
3 #
4 #------------------------------------------------------------------------------
5 # University of Minnesota
6 # Copyright 2017, Regents of the University of Minnesota
7 #------------------------------------------------------------------------------
8 # Author:
9 #
10 # James E Johnson
11 #
12 #------------------------------------------------------------------------------
13 """
14
15 import sys
16 import requests
17 from time import sleep
18
19
20 server = "https://rest.ensembl.org"
21 ext = "/info/assembly/homo_sapiens?"
22 max_region = 4000000
23
24
25 def ensembl_rest(ext, headers):
26 if True: print >> sys.stderr, "%s" % ext
27 r = requests.get(server+ext, headers=headers)
28 if r.status_code == 429:
29 print >> sys.stderr, "response headers: %s\n" % r.headers
30 if 'Retry-After' in r.headers:
31 sleep(r.headers['Retry-After'])
32 r = requests.get(server+ext, headers=headers)
33 if not r.ok:
34 r.raise_for_status()
35 return r
36
37
38 def get_species():
39 results = dict()
40 ext = "/info/species"
41 req_header = {"Content-Type": "application/json"}
42 r = ensembl_rest(ext, req_header)
43 for species in r.json()['species']:
44 results[species['name']] = species
45 print >> sys.stdout,\
46 "%s\t%s\t%s\t%s\t%s"\
47 % (species['name'], species['common_name'],
48 species['display_name'],
49 species['strain'],
50 species['taxon_id'])
51 return results
52
53
54 def get_biotypes(species):
55 biotypes = []
56 ext = "/info/biotypes/%s?" % species
57 req_header = {"Content-Type": "application/json"}
58 r = ensembl_rest(ext, req_header)
59 for entry in r.json():
60 if 'biotype' in entry:
61 biotypes.append(entry['biotype'])
62 return biotypes
63
64
65 def get_toplevel(species):
66 coord_systems = dict()
67 ext = "/info/assembly/%s?" % species
68 req_header = {"Content-Type": "application/json"}
69 r = ensembl_rest(ext, req_header)
70 toplevel = r.json()
71 for seq in toplevel['top_level_region']:
72 if seq['coord_system'] not in coord_systems:
73 coord_systems[seq['coord_system']] = dict()
74 coord_system = coord_systems[seq['coord_system']]
75 coord_system[seq['name']] = int(seq['length'])
76 return coord_systems
77
78
79 def get_transcripts_bed(species, refseq, start, length, strand='', params=None):
80 bed = []
81 param = params if params else ''
82 req_header = {"Content-Type": "text/x-bed"}
83 regions = range(start, length, max_region)
84 if not regions or regions[-1] < length:
85 regions.append(length)
86 for end in regions[1:]:
87 ext = "/overlap/region/%s/%s:%d-%d%s?feature=transcript;%s"\
88 % (species, refseq, start, end, strand, param)
89 start = end + 1
90 r = ensembl_rest(ext, req_header)
91 if r.text:
92 bed += r.text.splitlines()
93 return bed
94
95
96 def get_seq(id, seqtype,params=None):
97 param = params if params else ''
98 ext = "/sequence/id/%s?type=%s;%s" % (id, seqtype,param)
99 req_header = {"Content-Type": "text/plain"}
100 r = ensembl_rest(ext, req_header)
101 return r.text
102
103
104 def get_cdna(id,params=None):
105 return get_seq(id, 'cdna',params=params)
106
107
108 def get_cds(id,params=None):
109 return get_seq(id, 'cds',params=params)
110
111
112 def get_genomic(id,params=None):
113 return get_seq(id, 'genomic',params=params)
114
115
116 def get_transcript_haplotypes(species,transcript):
117 ext = "/transcript_haplotypes/%s/%s?aligned_sequences=1" % (species,transcript)
118 req_header = {"Content-Type" : "application/json"}
119 r = ensembl_rest(ext, req_header)
120 decoded = r.json()