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1 # A simple tool to connect to the AREsite server and retrieve feature
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2 # information using the AREsite REST Interface.
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3 # Parts of this code are from https://toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info
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4 from __future__ import print_function
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5
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6 import json
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7 import optparse
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8 import sys
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9 import urllib
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10 import urllib2
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11 import time
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12 import requests
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13 from six.moves.urllib.parse import urljoin
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14
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15 usage = "usage: %prog [options] arg1 arg2"
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16 parser = optparse.OptionParser(usage=usage)
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17 parser.add_option('-g', '--gene', help='Gene ID to search for')
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18 parser.add_option('-m', '--motif', help='Motif to look for', default='ATTTA', type=str)
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19 parser.add_option('-s', '--species', type='choice',
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20 choices=['Homo_sapiens', 'Mus_musculus', 'Danio_rerio', 'Drosophila_melanogaster', 'Caenorhabditis_elegans'], default='Homo_sapiens',
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21 help='Specify the species to investigate')
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22 options, args = parser.parse_args()
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23
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24 if options.gene is None:
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25 raise Exception('- Specify the gene you want to look for!')
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26
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27 if "," in options.motif :
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28 raise Exception('- Please only search for single motifs at once')
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29
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30 class AREsiteRestClient(object):
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31 def __init__(self, server='http://rna.tbi.univie.ac.at/AREsite2/api/', reqs_per_sec=1):
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32 self.server = server
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33 self.reqs_per_sec = reqs_per_sec
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34 self.req_count = 0
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35 self.last_req = 0
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36
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37 def perform_rest_action(self, endpoint, hdrs=None, params=None):
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38 if hdrs is None:
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39 hdrs = {}
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40
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41 if 'Content-Type' not in hdrs:
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42 hdrs['Content-Type'] = 'application/json'
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43
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44 if params:
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45 endpoint += '?' + urllib.urlencode(params)
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46
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47 data = None
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48
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49 # check if we need to rate limit ourselves
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50 if self.req_count >= self.reqs_per_sec:
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51 delta = time.time() - self.last_req
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52 if delta < 1:
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53 time.sleep(1 - delta)
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54 self.last_req = time.time()
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55 self.req_count = 0
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56
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57 try:
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58 request = urllib2.Request(self.server + endpoint, headers=hdrs)
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59 response = urllib2.urlopen(request)
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60 content = response.read()
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61 if content:
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62 data = json.loads(content)
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63 self.req_count += 1
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64
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65 except urllib2.HTTPError, e:
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66 # check if we are being rate limited by the server
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67 if e.code == 429:
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68 if 'Retry-After' in e.headers:
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69 retry = e.headers['Retry-After']
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70 time.sleep(float(retry))
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71 self.perform_rest_action(endpoint, hdrs, params)
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72 else:
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73 sys.stderr.write('Request failed for {0}: Status code: {1.code} Reason: {1.reason}\n'.format(endpoint, e))
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74
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75 return data
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76
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77 def get_motifs(self, species, gene, motifs):
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78 query = str('?query={0}&species={1}&list={2}'.format(gene, species, motifs))
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79 if query:
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80 aresite = self.perform_rest_action(
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81 query
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82 )
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83 return aresite
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84 return None
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85
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86 def run(species, gene, motifs):
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87 client = AREsiteRestClient()
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88 aresite = client.get_motifs(species, gene, motifs)
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89 if aresite:
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90
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91 mots = aresite["exact_motifs"]
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92 starts = aresite["motif_starts"]
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93 ends = aresite["motif_ends"]
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94 chrs = aresite["chromosomes"]
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95 strands = aresite["strands"]
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96 transcripts = aresite["transcripts"]
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97 genes = aresite["genes"]
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98 evh = aresite["hur_evidence"]
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99 evt = aresite["ttp_evidence"]
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100 eva = aresite["auf_evidence"]
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101 anno = aresite["annotation"]
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102
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103 aresite = zip(chrs,starts,ends,mots,anno,strands,genes,transcripts,evh,evt,eva)
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104
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105 def getKey(item):
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106 return item[1]
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107
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108 aresite = sorted(aresite, key=getKey)
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109
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110 # outfile = 'AREsite2_Rest_{0}_{1}_{2}.bed'.format(motifs,gene,species)
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111 # f = open(outfile, 'w')
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112
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113 for i in range(len(aresite)):
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114 # f.write("\t".join(aresite[i])+"\n")
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115 print ("\t".join(aresite[i])+"\n")
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116
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117
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118 if __name__ == '__main__':
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119 run(options.species, options.gene, options.motif)
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