Mercurial > repos > galaxyp > retrieve_ensembl_bed

annotate ensembl_rest.py @ 0:887e111c0919 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
author galaxyp
date Sun, 14 Jan 2018 14:11:53 -0500
parents
children c3d600729b6f
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0
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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1 #!/usr/bin/env python
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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2 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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3 #
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galaxyp
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4 #------------------------------------------------------------------------------
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
galaxyp
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5 # University of Minnesota
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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6 # Copyright 2017, Regents of the University of Minnesota
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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7 #------------------------------------------------------------------------------
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8 # Author:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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9 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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10 # James E Johnson
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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11 #
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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12 #------------------------------------------------------------------------------
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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13 """
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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14
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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15
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16 import sys
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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18 from time import sleep
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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20 import requests
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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23 server = "https://rest.ensembl.org"
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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24 ext = "/info/assembly/homo_sapiens?"
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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25 max_region = 4000000
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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26 debug = False
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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29 def ensembl_rest(ext, headers):
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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30 if debug:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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31 print >> sys.stderr, "%s" % ext
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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32 r = requests.get(server+ext, headers=headers)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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33 if r.status_code == 429:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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34 print >> sys.stderr, "response headers: %s\n" % r.headers
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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35 if 'Retry-After' in r.headers:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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36 sleep(r.headers['Retry-After'])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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37 r = requests.get(server+ext, headers=headers)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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38 if not r.ok:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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39 r.raise_for_status()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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40 return r
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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41
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42
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43 def get_species():
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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44 results = dict()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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45 ext = "/info/species"
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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46 req_header = {"Content-Type": "application/json"}
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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47 r = ensembl_rest(ext, req_header)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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48 for species in r.json()['species']:
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49 results[species['name']] = species
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50 print >> sys.stdout,\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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51 "%s\t%s\t%s\t%s\t%s"\
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52 % (species['name'], species['common_name'],
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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53 species['display_name'],
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54 species['strain'],
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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55 species['taxon_id'])
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56 return results
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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57
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58
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59 def get_biotypes(species):
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60 biotypes = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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61 ext = "/info/biotypes/%s?" % species
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62 req_header = {"Content-Type": "application/json"}
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63 r = ensembl_rest(ext, req_header)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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64 for entry in r.json():
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65 if 'biotype' in entry:
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66 biotypes.append(entry['biotype'])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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67 return biotypes
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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68
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69
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70 def get_toplevel(species):
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71 coord_systems = dict()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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72 ext = "/info/assembly/%s?" % species
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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73 req_header = {"Content-Type": "application/json"}
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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74 r = ensembl_rest(ext, req_header)
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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75 toplevel = r.json()
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76 for seq in toplevel['top_level_region']:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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77 if seq['coord_system'] not in coord_systems:
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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78 coord_systems[seq['coord_system']] = dict()
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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79 coord_system = coord_systems[seq['coord_system']]
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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80 coord_system[seq['name']] = int(seq['length'])
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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81 return coord_systems
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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82
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83
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84 def get_transcripts_bed(species, refseq, start, length, strand='',
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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85 params=None):
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86 bed = []
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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87 param = params if params else ''
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88 req_header = {"Content-Type": "text/x-bed"}
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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89 regions = range(start, length, max_region)
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90 if not regions or regions[-1] < length:
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91 regions.append(length)
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92 for end in regions[1:]:
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93 ext = "/overlap/region/%s/%s:%d-%d%s?feature=transcript;%s"\
887e111c0919 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 3fd7be931712e7fa5b281bc8c48104c8583ef7f0
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94 % (species, refseq, start, end, strand, param)
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95 start = end + 1
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96 r = ensembl_rest(ext, req_header)
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97 if r.text:
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98 bed += r.text.splitlines()
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99 return bed
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100
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101
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102 def get_seq(id, seqtype, params=None):
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103 param = params if params else ''
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104 ext = "/sequence/id/%s?type=%s;%s" % (id, seqtype, param)
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105 req_header = {"Content-Type": "text/plain"}
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106 r = ensembl_rest(ext, req_header)
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107 return r.text
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108
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109
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110 def get_cdna(id, params=None):
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111 return get_seq(id, 'cdna', params=params)
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112
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113
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114 def get_cds(id, params=None):
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115 return get_seq(id, 'cds', params=params)
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116
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117
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118 def get_genomic(id, params=None):
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119 return get_seq(id, 'genomic', params=params)
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120
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121
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122 def get_transcript_haplotypes(species, transcript):
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123 ext = "/transcript_haplotypes/%s/%s?aligned_sequences=1"\
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124 % (species, transcript)
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125 req_header = {"Content-Type": "application/json"}
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126 r = ensembl_rest(ext, req_header)
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127 decoded = r.json()
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128 return decoded