Mercurial > repos > rnateam > aresite2

comparison aresite2.py @ 0:6d3269dc319e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
author rnateam
date Thu, 02 Feb 2017 19:33:27 -0500
parents
children 138ff4068d27
comparison
equal deleted inserted replaced
-1:000000000000 0:6d3269dc319e
1 # A simple tool to connect to the AREsite server and retrieve feature
2 # information using the AREsite REST Interface.
3 # Parts of this code are from https://toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info
4 import json
5 import optparse
6 import sys
7 import urllib.request, urllib.parse, urllib.error
8 import urllib.request, urllib.error, urllib.parse
9 import time
10 import requests
11 from six.moves.urllib.parse import urljoin
12
13 usage = "usage: %prog [options] arg1 arg2"
14 parser = optparse.OptionParser(usage=usage)
15 parser.add_option('-g', '--gene', help='Gene ID to search for')
16 parser.add_option('-m', '--motif', help='Motif to look for', default='ATTTA', type=str)
17 parser.add_option('-s', '--species', type='choice',
18 choices=['Homo_sapiens', 'Mus_musculus', 'Danio_rerio', 'Drosophila_melanogaster', 'Caenorhabditis_elegans'], default='Homo_sapiens',
19 help='Specify the species to investigate')
20 options, args = parser.parse_args()
21
22 if options.gene is None:
23 raise Exception('- Specify the gene you want to look for!')
24
25 if "," in options.motif :
26 raise Exception('- Please only search for single motifs at once')
27
28 class AREsiteRestClient(object):
29 def __init__(self, server='http://rna.tbi.univie.ac.at/AREsite2/api/', reqs_per_sec=1):
30 self.server = server
31 self.reqs_per_sec = reqs_per_sec
32 self.req_count = 0
33 self.last_req = 0
34
35 def perform_rest_action(self, endpoint, hdrs=None, params=None):
36 if hdrs is None:
37 hdrs = {}
38
39 if 'Content-Type' not in hdrs:
40 hdrs['Content-Type'] = 'application/json'
41
42 if params:
43 endpoint += '?' + urllib.parse.urlencode(params)
44
45 data = None
46
47 # check if we need to rate limit ourselves
48 if self.req_count >= self.reqs_per_sec:
49 delta = time.time() - self.last_req
50 if delta < 1:
51 time.sleep(1 - delta)
52 self.last_req = time.time()
53 self.req_count = 0
54
55 try:
56 request = urllib.request.Request(self.server + endpoint, headers=hdrs)
57 response = urllib.request.urlopen(request)
58 content = response.read().decode('utf-8')
59 if content:
60 data = json.loads(content)
61 self.req_count += 1
62
63 except urllib2.HTTPError as e:
64 # check if we are being rate limited by the server
65 if e.code == 429:
66 if 'Retry-After' in e.headers:
67 retry = e.headers['Retry-After']
68 time.sleep(float(retry))
69 self.perform_rest_action(endpoint, hdrs, params)
70 else:
71 sys.stderr.write('Request failed for {0}: Status code: {1.code} Reason: {1.reason}\n'.format(endpoint, e))
72
73 return data
74
75 def get_motifs(self, species, gene, motifs):
76 query = str('?query={0}&species={1}&list={2}'.format(gene, species, motifs))
77 if query:
78 aresite = self.perform_rest_action(
79 query
80 )
81 return aresite
82 return None
83
84 def run(species, gene, motifs):
85 client = AREsiteRestClient()
86 aresite = client.get_motifs(species, gene, motifs)
87 if aresite:
88
89 mots = aresite["exact_motifs"]
90 starts = aresite["motif_starts"]
91 ends = aresite["motif_ends"]
92 chrs = aresite["chromosomes"]
93 strands = aresite["strands"]
94 transcripts = aresite["transcripts"]
95 genes = aresite["genes"]
96 evh = aresite["hur_evidence"]
97 evt = aresite["ttp_evidence"]
98 eva = aresite["auf_evidence"]
99 anno = aresite["annotation"]
100
101 aresite = zip(chrs,starts,ends,mots,anno,strands,genes,transcripts,evh,evt,eva)
102
103 def getKey(item):
104 return item[1]
105
106 aresite = sorted(aresite, key=getKey)
107
108 for site in aresite:
109 print("\t".join(site))
110
111
112 if __name__ == '__main__':
113 run(options.species, options.gene, options.motif)