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annotate ensembl_rest.py @ 0:038ecf54cbec draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
author galaxyp
date Mon, 22 Jan 2018 13:59:27 -0500
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0
038ecf54cbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
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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 from __future__ import print_function
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16 from __future__ import unicode_literals
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17
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18 import sys
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20 from time import sleep
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22 import requests
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25 server = "https://rest.ensembl.org"
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26 ext = "/info/assembly/homo_sapiens?"
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27 max_region = 4000000
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28 debug = False
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31 def ensembl_rest(ext, headers):
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32 if debug:
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33 print("%s" % ext, file=sys.stderr)
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34 r = requests.get(server+ext, headers=headers)
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35 if r.status_code == 429:
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36 print("response headers: %s\n" % r.headers, file=sys.stderr)
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37 if 'Retry-After' in r.headers:
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38 sleep(r.headers['Retry-After'])
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39 r = requests.get(server+ext, headers=headers)
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40 if not r.ok:
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41 r.raise_for_status()
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42 return r
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43
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44
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45 def get_species():
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46 results = dict()
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47 ext = "/info/species"
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48 req_header = {"Content-Type": "application/json"}
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49 r = ensembl_rest(ext, req_header)
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50 for species in r.json()['species']:
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51 results[species['name']] = species
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52 print("%s\t%s\t%s\t%s\t%s" %
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53 (species['name'], species['common_name'],
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54 species['display_name'],
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55 species['strain'],
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56 species['taxon_id']), file=sys.stdout)
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57 return results
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58
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59
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60 def get_biotypes(species):
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61 biotypes = []
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62 ext = "/info/biotypes/%s?" % species
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63 req_header = {"Content-Type": "application/json"}
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64 r = ensembl_rest(ext, req_header)
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65 for entry in r.json():
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66 if 'biotype' in entry:
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67 biotypes.append(entry['biotype'])
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68 return biotypes
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69
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70
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71 def get_toplevel(species):
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72 coord_systems = dict()
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73 ext = "/info/assembly/%s?" % species
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74 req_header = {"Content-Type": "application/json"}
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75 r = ensembl_rest(ext, req_header)
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76 toplevel = r.json()
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77 for seq in toplevel['top_level_region']:
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78 if seq['coord_system'] not in coord_systems:
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79 coord_systems[seq['coord_system']] = dict()
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80 coord_system = coord_systems[seq['coord_system']]
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81 coord_system[seq['name']] = int(seq['length'])
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82 return coord_systems
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83
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84
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85 def get_transcripts_bed(species, refseq, start, length, strand='',
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86 params=None):
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87 bed = []
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88 param = params if params else ''
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89 req_header = {"Content-Type": "text/x-bed"}
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90 regions = list(range(start, length, max_region))
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91 if not regions or regions[-1] < length:
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92 regions.append(length)
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93 for end in regions[1:]:
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94 ext = "/overlap/region/%s/%s:%d-%d%s?feature=transcript;%s"\
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95 % (species, refseq, start, end, strand, param)
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96 start = end + 1
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97 r = ensembl_rest(ext, req_header)
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98 if r.text:
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99 bed += r.text.splitlines()
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100 return bed
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101
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102
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103 def get_seq(id, seqtype, params=None):
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104 param = params if params else ''
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105 ext = "/sequence/id/%s?type=%s;%s" % (id, seqtype, param)
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106 req_header = {"Content-Type": "text/plain"}
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107 r = ensembl_rest(ext, req_header)
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108 return r.text
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109
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110
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111 def get_cdna(id, params=None):
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112 return get_seq(id, 'cdna', params=params)
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113
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114
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115 def get_cds(id, params=None):
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116 return get_seq(id, 'cds', params=params)
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117
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118
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119 def get_genomic(id, params=None):
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120 return get_seq(id, 'genomic', params=params)
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121
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122
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123 def get_transcript_haplotypes(species, transcript):
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124 ext = "/transcript_haplotypes/%s/%s?aligned_sequences=1"\
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125 % (species, transcript)
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126 req_header = {"Content-Type": "application/json"}
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127 r = ensembl_rest(ext, req_header)
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128 decoded = r.json()
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129 return decoded