Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/galaxy/genomes/__init__.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 Contains possible interactions with the Galaxy Histories |
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3 """ |
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4 from bioblend.galaxy.client import Client |
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5 |
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6 |
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7 class GenomeClient(Client): |
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8 |
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9 def __init__(self, galaxy_instance): |
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10 self.module = 'genomes' |
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11 super().__init__(galaxy_instance) |
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12 |
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13 def get_genomes(self): |
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14 """ |
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15 Returns a list of installed genomes |
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16 |
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17 :rtype: list |
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18 :return: List of installed genomes |
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19 """ |
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20 genomes = self._get() |
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21 return genomes |
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22 |
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23 def show_genome(self, id, num=None, chrom=None, low=None, high=None): |
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24 """ |
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25 Returns information about build <id> |
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26 |
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27 :type id: str |
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28 :param id: Genome build ID to use |
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29 |
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30 :type num: str |
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31 :param num: num |
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32 |
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33 :type chrom: str |
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34 :param chrom: chrom |
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35 |
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36 :type low: str |
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37 :param low: low |
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38 |
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39 :type high: str |
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40 :param high: high |
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41 |
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42 :rtype: dict |
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43 :return: Information about the genome build |
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44 """ |
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45 params = {} |
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46 if num: |
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47 params['num'] = num |
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48 if chrom: |
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49 params['chrom'] = chrom |
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50 if low: |
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51 params['low'] = low |
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52 if high: |
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53 params['high'] = high |
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54 return self._get(id, params) |
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55 |
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56 def install_genome(self, func='download', source=None, dbkey=None, |
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57 ncbi_name=None, ensembl_dbkey=None, url_dbkey=None, |
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58 indexers=None): |
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59 """ |
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60 Download and/or index a genome. |
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61 |
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62 |
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63 :type dbkey: str |
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64 :param dbkey: DB key of the build to download, ignored unless 'UCSC' is specified as the source |
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65 |
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66 :type ncbi_name: str |
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67 :param ncbi_name: NCBI's genome identifier, ignored unless NCBI is specified as the source |
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68 |
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69 :type ensembl_dbkey: str |
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70 :param ensembl_dbkey: Ensembl's genome identifier, ignored unless Ensembl is specified as the source |
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71 |
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72 :type url_dbkey: str |
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73 :param url_dbkey: DB key to use for this build, ignored unless URL is specified as the source |
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74 |
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75 :type source: str |
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76 :param source: Data source for this build. Can be: UCSC, Ensembl, NCBI, URL |
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77 |
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78 :type indexers: list |
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79 :param indexers: POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) |
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80 |
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81 :type func: str |
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82 :param func: Allowed values: 'download', Download and index; 'index', Index only |
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83 |
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84 :rtype: dict |
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85 :return: dict( status: 'ok', job: <job ID> ) |
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86 If error: |
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87 dict( status: 'error', error: <error message> ) |
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88 """ |
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89 payload = {} |
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90 if source: |
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91 payload['source'] = source |
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92 if func: |
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93 payload['func'] = func |
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94 if dbkey: |
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95 payload['dbkey'] = dbkey |
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96 if ncbi_name: |
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97 payload['ncbi_name'] = ncbi_name |
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98 if ensembl_dbkey: |
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99 payload['ensembl_dbkey'] = ensembl_dbkey |
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100 if url_dbkey: |
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101 payload['url_dbkey'] = url_dbkey |
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102 if indexers: |
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103 payload['indexers'] = indexers |
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104 return self._post(payload) |