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